Human pluripotent stem cells produced by somatic cell nuclear transfer

ABSTRACT

Human pluripotent embryonic stem cells produced by somatic cell nuclear transfer as well as methods of making and using said human pluripotent embryonic stem cells are disclosed.

PRIORITY CLAIM

This application claims the benefit of U.S. Provisional PatentApplication 61/822,707, filed 13 May 2013.

FIELD

Generally, the field is human pluripotent stem cells. More specifically,the field is human pluripotent stem cells produced by somatic cellnuclear transfer and methods of making and using the same.

BACKGROUND

Cytoplasmic factors present in mature metaphase II arrested (MII)oocytes have a unique activity to reset the identity of transplantedsomatic cell nuclei to the embryonic state. Since the initial discoveryin amphibians (Gurdon J B, J Embryology, Exp Morphology 10, 622-640(1962)), SCNT success in a range of different mammalian speciesdemonstrated that this reprogramming activity in enucleated oocytes(cytoplasts) is universal (Solter D, Nat Rev Genet 1, 199-207 (2000) andWilmut I et al, Nature 419, 583-586 (2002)). However, despite numerousapplications of SCNT for animal cloning, the nature of reprogrammingoocyte factors and the mechanism of their action remain largely unknown.

Pluripotent stem cells have been produced by somatic cell nucleartransfer in non-human primates (U.S. Pat. No. 7,972,849.) In humans,SCNT has been envisioned as a method of generating personalizedembryonic stem cells from a patient's somatic cells that could be usedto study the mechanisms of disease and ultimately to be used for cellbased therapies (Lanza R P et al, Nature Biotech 17, 1171-1174 (1999)and Yang X et al, Nature Genet 39, 295-302 (2007)). However, derivationof human nuclear transfer derived ESCs (NT-ESCs) has not been achieved,despite numerous attempts over the past decade.

SUMMARY

Disclosed herein is the production of human embryonic stem cells derivedfrom somatic cell nuclear transfer. The method of producing the cellsinvolves: enucleating a human oocyte by removing the MII spindle by anymanner that does not lower levels of maturation promoting factor. Thisaction produces a cytoplast. A polarized microscope can be used in thisprocedure. The method further involves contacting a human donor nucleuswith an HVJ-E extract and also contacting the cytoplast with the humandonor nucleus, thereby producing an SCNT embryo. The donor nucleus canbe provided in the context of a donor cell, such as a fibroblast. Insome aspects of the method, the donor cell can be treated with aprotease such as trypsin, thereby producing a disaggregated donor cell.

In addition, the method involves treating the human oocyte and/or thecytoplast and/or the SCNT embryo with a protein phosphatase inhibitor.The protein phosphatase can be any protein phosphatase inhibitor,including caffeine. In some aspects, the protein phosphatase inhibitoris present during both the enucleation of the human oocyte and thecontacting of the SCNT embryo with the donor nucleus. In furtheraspects, the caffeine is present at a concentration of at least 1.25 mM.In still further aspects, the caffeine is present at a concentration ofbetween 1.25 mM and 2.5 mM.

The method further involves applying at least one electroporation pulseto the SCNT embryo, thereby activating the SCNT embryo. The activatedSCNT embryo is cultured in a first media that includes 6-DMAP. Theactivated SCNT embryo is cultured in a second media that includes TSA.The activated SCNT embryo is then cloned in a third media, therebyproducing a blastocyst. The blastocyst is cultured on a feeder layer,and then cells with embryonic stem cell like morphologies are selected.In further aspects, the cells with embryonic stem cell like morphologiesare further characterized as having donor nucleus nuclear DNA and oocytedonor mitochondrial DNA.

In some aspects, particular oocytes are selected including oocytes froma donation cycle of 15 or fewer oocytes, from donation cycles of 10 orfewer oocytes, or from oocyte donors treated with a GnRH inhibitor suchas ganirelix. In further aspects, the method involves collecting thehuman oocyte from the oocyte donor.

It is an object of the invention to provide human pluripotent stem cellsthat have improved epigenetic reprogramming relative to those producedby transcription-factor based reprogramming (induced pluripotent stemcells).

It is an object of the invention to provide human pluripotent stem cellsthat are genetically identical to a subject providing a donor nucleusthat are more similar to human pluripotent stem cells produced by invitro fertilization than those produced by transcription-factor basedreprogramming.

BRIEF DESCRIPTION OF THE DRAWINGS

Some of the drawings in this disclosure are photographic images thatcannot reproduce properly in a patent application publication.Additionally, some of the drawings can be better understood when viewedin color, which is not available in a patent application publication.Applicants consider all photographic images and color drawings as partof the original disclosure and reserve the right to present high qualityand/or color images of the herein described figures in laterproceedings.

FIGS. 1A, 1B, and 1C collectively show optimization of SCNT protocolsusing a rhesus monkey model.

FIG. 1A is a cartoon and image depicting the effect of donor cellintroduction by electrofusion or HVJ-E fusion on somatic cell nuclearremodeling. NEBD and PCC were associated with HVJ-E-based fusion but notwith electrofusion.

FIG. 1B is a cartoon depicting a schematic representation of a studytesting for the results of electroporation on proper activation and SCNTblastocyst formation.

FIG. 1C is a bar graph depicting the results of the study in FIG. 1B.(See also FIG. 8, and Tables 1 and 2).

FIGS. 2A, 2B, 2C, 2D, 2E, and 2F collectively show that SCNT blastocystdevelopment is affected by premature cytoplast activation.

FIG. 2A is an image depicting the morphology of nuclear donor fetalfibroblasts before SCNT.

FIG. 2B is an image depicting a poor quality human SCNT blastocystwithout distinct ICM.

FIG. 2C is an image depicting spindle-like structures detected whendonor nuclei are introduced into intact MII oocytes but not afterenucleation. Arrowhead and arrow point at the maternal MII spindle andsomatic cell spindle, respectively.

FIG. 2D is an image depicting somatic cell spindles formed in cytoplastswhen oocyte enucleation and fusion were conducted in presence ofcaffeine.

FIG. 2E is an image depicting a human SCNT blastocyst with a prominentICM (asterisk) produced after caffeine treatment.

FIG. 2F is an image depicting a NT-ESC colony with typical ESCmorphology derived from caffeine treated SCNT human embryos.

FIGS. 3A and 3B collectively show the development of human SCNT embryosand NT-ESC derivation after caffeine treatment.

FIG. 3A is a bar graph depicting the percentage of SCNT embryosdeveloping into blastocysts with and without caffeine treatment.

FIG. 3B is a bar graph depicting the development of NT-ESCs fromblastocysts with and without caffeine treatment.

FIGS. 4A and 4B collectively show the results from human SCNT from donorcells derived from a patient with Leigh's disease.

FIG. 4A is a bar graph depicting vitro development of SCNT embryosproduced with skin cells from Leigh's disease patient. The donor cellswere fused with embryos from two different oocyte donors as indicated.Fifteen MII oocytes were retrieved from egg donor #11 and only fiveoocytes were collected from the donor #12. SCNT blastocysts weregenerated from both oocyte cohorts.

FIG. 4B is a bar graph depicting the NT-ESC derivation efficiency fromoocytes from each donor.

FIGS. 5A, 5B, 5C and 5D collectively depict the effect of ovarianstimulation on human SCNT outcomes.

FIG. 5A is a bar graph depicting human SCNT development groupedaccording to the number of oocytes collected from each cycle. Cyclesproducing 10 or less oocytes were associated with improved developmentof SCNT embryos.

FIG. 5B is a bar graph depicting the result that the efficacy of NT-ESCderivation is dependent on the number of oocytes collected from a cycle.

FIG. 5C is a bar graph depicting the outcome of SCNT embryo developmentgrouped according to whether or not the oocyte donor received a GnRHagonist or a GnRH antagonist. Blastocyst development was improved fromoocyte donors receiving a GnRH antagonist.

FIG. 5D is a bar graph depicting the outcome of NT-ESCs groupedaccording to whether or not the oocyte donor received a GnRH agonist ora GnRH antagonist.

FIGS. 6A, 6B, 6C, 6D, and 6E collectively show the genetic, cytogenetic,and pluripotency analyses of human NT-ESCs

FIG. 6A is a table depicting the results of nuclear DNA genotyping fromfour human NT-ESC lines (hESO-NT1, -NT2, -NT3 and -NT4) determined bymicrosatellite parentage analysis. A total of 24 microsatellite markerswere used for each cell typing. The representative markers for D2S1333and D4S413 loci demonstrate that the nuclear DNA in these cell lines wasexclusively derived from the somatic HDF-f cell line. No contribution ofoocyte nuclear DNA was detected.

FIG. 6B, is a trace resulting from mtDNA genotyping by Sanger sequencingwhich demonstrated that all NT-ESC lines contain oocyte mtDNA.

FIG. 6C is an image of the results of a cytogenetic G-banding analysisthat confirmed all NT-ESCs exhibit normal 46XX karyotype.

FIG. 6D is a set of 8 images showing that human NT-ESCs express standardpluripotency markers detected by immunocytochemistry for antibodiesagainst OCT4, NANOG, SOX2, SSEA4, TRA-1-60 and TRA-1-81. Originalmagnification was 200×.

FIG. 6E is a set of two images depicting histological analysis ofteratoma tumors produced after injection of human NT-ESCs into SCIDmice. An arrow and arrowhead in the upper panel indicate Intestinal-typeepithelium with goblet cells (endoderm) and cartilage (mesodermal),respectively. An arrow and arrowhead in the lower panel depictneuroectodermal (ectoderm) and muscle (mesoderm) tissues, respectively.Original magnification was ×200.

FIGS. 7A and 7B collectively show microarray expression analysis ofhuman NT-ESC's.

FIG. 7A is a scatter plot analysis comparing expression profiles ofhuman NT-ESCs (hESO-NT1) with IVF-derived ESC controls (hESO-7) andparental dermal fibroblasts (HDF-f). NT-ESCs displayed lowtranscriptional correlation to fibroblasts but were similar to ESCsderived from fertilized embryos.

FIG. 7B is a tree diagram depicting the linkages between NT-ESCs andIVF-ESCs.

FIG. 8 is a bar graph depicting the In vitro development of monkey SCNTembryos with or without electro pulse, and various concentrations of TSAas indicated.

FIG. 9A is a bar graph depicting the in vitro development of SCNTembryos from a human donor to the blastocyst stage.

FIG. 9B is a bar graph depicting the in vitro development of pluripotentstem cell lines from SCNT embryos from the same human donor as in FIG.9A.

FIG. 10 is a bar graph depicting the correlation between peak estradiollevels and the numbers of MII oocytes produced by human donors.

FIG. 11 is a chart with images that illustrates in vitro development andstem cell isolation of different subcategories at pronuclearobservation.

FIG. 12A is an image of a chromosome G-banding analysis for the hESO-NT2line.

FIG. 12B is an image of a chromosome G-banding analysis for the hESO-NT3line.

FIG. 12C is an image of a chromosome G-banding analysis for the hESO-NT4line.

FIG. 13 is a set of images resulting from a pluripotency analysis inhuman ESCs derived from conventional IVF (hESO-7&-8) and SCNT (hESO-NT2,-3 and -4).

FIG. 14 is a set of nine microarray scatter plots used for comparisonsof biological replications.

FIG. 15A is a representation of a principal component analysis ofIVF-ESCs (red balls), iPSCs (yellow and orange balls), and NT-ESCs(green balls) with nearest neighbor analysis.

FIG. 15B is a table showing the total number of differentiallymethylated probes (DMPs) observed between matched iPSCs, NT-ESCs andIVF-ESCs (n=11). The number of DMPs shared with parental HDFs was usedas a measure of the degree somatic cell memory.

FIG. 16A is a heat map of previously identified imprinted regions. Foreach gene, an average β-value for all methylation probes assigned to aspecific gene is shown and the number of included probes is indicatednext to the gene. White box: hypermethylation at DIRAS3 locus, no changein gene expression; black boxes: DNA methylation changes at H19,GNASAS/GNAS, and GNAS loci, no change in gene expression; grey box:hypermethylation at the MEG3 locus, reduced gene expression; yellow box:hypermethylation at the PEG3 locus, reduced gene expression.

FIG. 16B is a bar graph showing percentage of total imprinted probesthat had a β<0.2 or β>0.8.

FIG. 16C is a set of two bar/line graphs showing the normalized RNA-Seqread count (bars, averaged between replicates) and the methylationβ-values (black line) for MEG3 and PEG3.

FIG. 17A is a heat map displaying β-values of previously identified XCIprobes on the methylation array in NT-ESCs, IVF-ESCs, iPSCs, and HDFs.The genes highlighted with black boxes showed both aberranthypermethylation and gene expression alteration. The hypomethylatedgenes highlighted in white boxes were associated with gene expressionalteration.

FIG. 17B is a Line graph showing an average β-value for all XCI probesfor each cell line (Two-sided t-test P<0.001, error bars s.e.m.). c, Thepercentage of total XCI probes with β<0.2 or β>0.8 (Two-sided t-testP<0.001).

FIG. 18A is a complete hierarchical clustering of CG methylation for atotal 678 CG-DMRs identified by comparing methylomes of NT-ESCs andiPSCs to IVF-ESCs methylomes.

FIG. 18B is a Venn diagram showing the overlap of CG-DMRs across iPSCsand NT-ESCs in cases where the DMR is found in at least one of the linesin the same group.

FIG. 18C is a bar graph showing the number of 678 CG-DMRs overlapped (1bp) with indicated genomic features—CGI, CG islands; TSS, transcriptionstart sites; TES, transcription end sites.

FIG. 18D is a bar graph showing the distribution of CG-DMRs among eachNT-ESC and iPSC line. DMRs that were also shared with parental somaticcells were identified as memory or mDMRs. ntDMRs—NT-specific andiDMRs-iPSC-specific.

FIG. 18E is a Venn diagram showing the hotspot CG-DMRs that wereidentified in every iPSC or NT-ESC line in the same group. 48 hotspotCG-DMRs were shared among all iPSC and NT-ESC lines.

FIG. 19A is a Venn diagram showing the overlap of the 77 non-CGmega-DMRs identified in the iPSC and the NT-ESC lines from this study.Numbers within circles denote DMRs identified exclusively within eachgroup. Five DMRs were shared among all cell lines in both groups.

FIG. 19B is a chromosome ideogram showing the location of the 77 non-CGmega-DMRs found in both NT-ESC and iPSC lines from this study. Orangecircles and lines indicate the location of the individual DMRs specificfor iPSCs; green circles and lines denote those specific for NT-ESCs andyellow circles and lines are DMRs shared by both cell types.

FIG. 19C is a bar graph showing the total length of the non-CG mega-DMRsidentified in 4 NT-ESC, and 9 iPSC lines. The NT-ESCs had asignificantly lower size of DMRs (Mann-Whitney test, P<0.005) comparedto the iPSCs.

FIG. 19D is a bar graph showing the total number of the non-CG mega-DMRsidentified in the cell lines. The NT-ESCs had a significantly lowernumber of DMRs (Mann-Whitney test, P<0.005) compared to the iPSCs.

FIG. 20A is a heat map displaying 1220 differentially expressed genesbetween NT-ESCs, iPSCs and IVF-ESCs (n=22) (ANOVA adjustedp-value<0.05). Genes were clustered into ten groups for functionalanalysis and presented as a heat map (on the right). Cluster 4, 6, 7,and 9 showed no significant functional enrichments.

FIG. 20B is a Venn diagram showing the number of genes differentiallyexpressed between the HDF and the IVF-ESCs (large circle), the iPSCs andthe IVF-ESCs (medium circle) and the NT-ESCs and IVF-ESCs (slam circle;t-test FDR<0.05). Overlapping regions represent the number of genesdifferentially expressed in both the HDF and either the NT-ESCs oriPSCs.

FIG. 20C is a set of Notched box plots represent the β value of allprobes in the promoter regions (−2000 bp to 500 bp) of the genes thatwere expressed at significantly lower levels (t-test FDR<0.05) in boththe HDFs and the iPSCs (exhibiting transcriptional memory) when comparedto the IVF-ESCs. The box represents the interquartile range (25th to75th percentile), and the line within the box marks, the median. Thenotch in the box represents the 95% confidence interval around themedian. The whiskers above and below the box contain 99.3% of the dataand the number of CpGs interrogated is shown on the y-axis.

DETAILED DESCRIPTION

Human pluripotent stem cells produced by somatic cell nuclear transferare disclosed herein. Methods of making and using these pluripotent stemcells are also disclosed.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as is commonly understood by one of ordinary skillin the art to which this invention belongs.

The term “nuclear genetic material” refers to structures and/ormolecules found in the nucleus that comprise polynucleotides (e.g., DNA)that encode information about the individual. Nuclear genetic materialincludes, but is not limited to, chromosomes and chromatin. The termincludes nuclear genetic material produced by cell division such as thedivision or a parental cell into daughter cells. Thus, a cell includesnuclear genetic material derived from a donor somatic cell if the cellhas been produced during mitosis or meiosis from an original cell, or ifthe nuclear genetic material has been transferred into an enucleatedcytoplast via somatic cell nuclear transfer.

The term “mitochondrial DNA” or “mtDNA” refers to the DNA of themitochondrion, a structure situated in the cytoplasm of the cell ratherthan in the nucleus (where all the other chromosomes are located). Invivo, all mtDNA is inherited from the mother. There are 2 to 10 copiesof the mtDNA genome in each mitochondrion. Mitochondrial DNA is adouble-stranded, circular molecule. It is very small relative to thechromosomes in the nucleus and includes only a limited number of genes,such as those encoding a number of the subunits in the mitochondrialrespiratory-chain complex and the genes for some ribosomal RNAs andtransfer RNAs. A cell includes mtDNA derived from the continuedreplication cytoplasmically based mitochondria, which in the case ofSCNT are based in the recipient cytoplast.

The term “DNA methylation” refers to the postsynthetic addition ofmethyl groups to specific sites on DNA molecules; the reaction iscatalyzed by enzymes called DNA methyltransferases that are specific fornucleotide and position of methylation. In eukaryotes, methylation isinvolved in gene expression, and plays a role in a variety of epigeneticmechanisms, including development, X chromosome inactivation, genomicimprinting, mutability of DNA, and uncontrolled cell growth in cancer.

The term “X chromosome inactivation” refers to the inactivation of oneof each pair of X chromosomes to form the Barr body in female mammaliansomatic cells. Thus tissues whose original zygote carried heterozygous Xborne genes should have individual cells expressing one or other but notboth of the X encoded gene products. The inactivation is thought tooccur early in development and leads to mosaicism of expression of suchgenes in the body.

The phrase “dosage compensation” refers to a mechanism that senses genedosage and regulates expression accordingly. In mammals there ismonoallelic expression of X-linked genes that differ in dose betweenfemales (XX) and males (XY). “XIST” refers to a gene encoding a largenon-coding RNA which has been shown to be necessary for developmentallyregulated X chromosome silencing in females. The XIST RNA is about 18 kband is not translated, it is spliced, and polyadenylated. It is alsoorganized into blocks of repetitive sequence. In vivo, XIST RNA is foundto be stably associated with the silenced X chromosome. The expressionof XIST RNA is always cis-limited, and is associated with the silenced Xchromosome in females.

The term “effective amount” or “therapeutically effective amount” refersto the amount of agent or a cell that is sufficient to prevent, treat,reduce and/or ameliorate the symptoms and/or underlying causes of anydisorder or disease, or the amount of an agent sufficient to produce adesired effect on a cell. In one embodiment, a “therapeuticallyeffective amount” is an amount of a cell or an agent sufficient toreduce or eliminate a symptom of a disease. In another embodiment, atherapeutically effective amount is an amount sufficient to overcome thedisease itself.

As used herein, the term “preparation,” “purified preparation,”“isolated preparation,” “isolated population” or “purified population”of pluripotent human stem cells refers to a preparation of one or morecells that has been manipulated to provide a preparation of cells thatis substantially free of additional components. In some embodiments, thecell preparation is at least about 60%, by weight or number, free fromother components that are present when the cell is produced, such asother types of cells. In various embodiments, the cell is at least about75%, or at least about 85%, or at least about 90%, or at least about95%, or at least about 99%, by weight or number, pure. A purified cellpreparation can be obtained, for example, by purification (e.g.,extraction) from a natural source, fluorescence-activated cell-sorting,or other techniques known to the skilled artisan. Purity can be assayedby any appropriate method, such as fluorescence-activated cell sorting(FACS) or by visual examination.

The cells described herein progress through a series of divisions into ablastocyst in vitro. The blastocyst comprises an inner cell mass (ICM)and a trophoblast. The cells found in the ICM give rise to pluripotentstem cells that possess the ability to proliferate indefinitely, or ifproperly induced, differentiate in all cell types contributing to anorganism.

As used herein, the term “pluripotent” refers to a cell's potential todifferentiate into cells of the three germ layers: endoderm (e.g.,interior stomach lining, gastrointestinal tract, the lungs), mesoderm(e.g., muscle, bone, blood, urogenital), or ectoderm (e.g., epidermaltissues and nervous system). Pluripotent stem cells can give rise to anyfetal or adult cell type including germ cells. However, PSCs alonecannot develop into a fetal or adult animal when transplanted in uterobecause they lack the potential to contribute to extra embryonic tissue(e.g., placenta in vivo or trophoblast in vitro).

PSCs are the source of multipotent stem cells (MPSCs) which arisethrough spontaneous differentiation or as a result of exposure todifferentiation induction conditions in vitro. The term “multipotent”refers to a cell's potential to differentiate and give rise to a limitednumber of related, different cell types. These cells are characterizedby their multi-lineage potential and the ability for self-renewal. Invivo, the pool of MPSCs replenishes the population of maturefunctionally active cells in the body. Among the exemplary MPSC typesare hematopoietic, mesenchymal, or neuronal stem cells.

Transplantable cells include MPSCs and more specialized cell types suchas committed progenitors as well as cells further along thedifferentiation and/or maturation pathway that are partly or fullymatured or differentiated. “Committed progenitors” give rise to a fullydifferentiated cell of a specific cell lineage. Exemplary transplantablecells include pancreatic cells, epithelial cells, cardiac cells,endothelial cells, liver cells, endocrine cells, and the like.

A “feeder layer” refers to non-proliferating cells (such as irradiatedcells) that can be used to support proliferation of pluripotent stemcells. Protocols for the production of feeder layers are known in theart, and are available on the internet, such as at the National StemCell Resource website, which is maintained by the American Type CultureCollection (ATCC).

As used herein, the term “embryo” refers generally to a cellular massobtained by one or more divisions of a zygote or an activated oocytewith an artificially reprogrammed nucleus. A “morula” is thepreimplantation embryo 3-4 days after fertilization, when it is a solidmass, generally composed of 12-32 cells (blastomeres). A “blastocyst”refers to a preimplantation embryo in placental mammals (about 3 daysafter fertilization in the mouse, about 5 days after fertilization inhumans) of about 30-150 cells. The blastocyst stage follows the morulastage, and can be distinguished by its unique morphology. The blastocystis generally a sphere made up of a layer of cells (the trophectoderm), afluid-filled cavity (the blastocoel or blastocyst cavity), and a clusterof cells on the interior (the ICM).

“Genomic imprinting” refers to a mammalian epigenetic phenomenon wherebythe parental origin of a gene determines whether or not it will beexpressed. Over 75 imprinted genes have been identified, many of whichare noncoding RNAs that are hypothesized to control the expression oflinked protein coding genes that are also imprinted. Generally,allele-specific methylation of CpG dinucleotides is a mechanism thatregulates gene expression of imprinted genes. “Maternally expressed”refers to a gene that is expressed from the copy inherited from themother. Imprinted genes include, but are not limited to the maternallyexpressed imprinted genes H19, CDKNIC, PHLDA2, DLXS, ATP10A, SLC22A18 orTP73. Paternally expressed imprinted genes include but are not limitedto IGF2, NDN, SNRPN, MEST, MAGEL2, and PEG3. Exemplary sequenceinformation for these genes, including the human nucleic acid sequences,can be found at the gene imprint website, available on the Internet.

Lamin refers to the major non-collagenous component of the basal lamina.It is a glycoprotein that has an “A” chain and two “B” chains. Laminsare fibrous proteins providing structural function and transcriptionalregulation in the cell nucleus. A-type lamins are only expressedfollowing gastrulation. Lamins A and C are the most common A-type laminsand are splice variants of the LMNA gene.

“Maturation promoting factor” (MPF) refers to a heterodimeric proteincomprising cyclin B and cyclin-dependent kinase 1 (p34cdc2) thatstimulates the mitotic and meiotic cell cycles. MPF promotes theentrance into mitosis from the G2 phase by phosphorylating multipleproteins needed during mitosis. MPF is activated at the end of G2 by aphosphatase which removes an inhibitory phosphate group added earlier.Targets for MPF include condensing, which enable chromatin condensation;various microtubule-associated proteins involved in mitotic spindleformation; lamins, whose interaction contribute to the degradation ofthe nuclear envelope as well as the histones H1 and H3; and the Golgimatrix, to cause fragmentation.

“Nuclear reprogramming” results in immediate inhibition of transcriptionin the transferred somatic cell nucleus and the subsequent establishmentof temporal and spatial patterns of embryonic gene expression associatedwith normal development. Currently unidentified reprogramming factorspresent in oocytes are capable of initiating a cascade of events thatcan reset the epigenetic program of specialized somatic cells back to anundifferentiated state.

“Nuclear remodeling” refers to morphological and biochemical changes innuclear material occurring soon after introduction of somatic cellnucleus into an enucleated, nonactivated, mature oocyte. Nuclearremodeling includes but is not confined to nuclear envelope breakdown(NEBD), followed by premature chromosome condensation (PCC) and spindleformation.

“Nuclear transfer” refers to the insertion of a donor nucleus into anenucleated recipient host cell.

“Telomere” refers to the sequences and the ends of a eukaryoticchromosome, consisting of many repeats of a short DNA sequence inspecific orientation. Telomere functions include protecting the ends ofthe chromosome so that chromosomes do not end up joined together andallowing replication of the extreme ends of the chromosomes (bytelomerase). The number of repeats of telomeric DNA at the end of achromosome decreases with age and telomeres play roles in aging andcancer. “Telomerase” refers to a DNA polymerase involved in theformation of telomeres and the maintenance of telomere sequences duringchromosome replication.

“HVJ-E extract” refers to inactivated viral envelope from theHaemagglutinating virus of Japan. HVJ is also referred to as Sendaivirus.

“6-DMAP” refers to 6-Dimethylaminopurine.

“TSA” refers to trichostatin A.

Human Pluripotent and Multipotent Stem Cells

Compositions of human PSCs are provided herein. The PSCs are capable ofextended propagation in vitro without losing their ability todifferentiate into ectoderm, mesoderm and endoderm. The PSCs can havebeen generated and stored in the course of their use and/or propagation,such as by freezing. These PSCs can be isolated, and thus can bepropagated in vitro.

In some examples, the human PSCs are capable of proliferating for atleast 4 or more cell divisions in vitro wherein the PSC maintains itspluripotency. In other embodiments, the PSCs are capable ofproliferating at least 5, 6, 7, 8 or more cell divisions, wherein thePSCs maintain their pluripotency. In other examples, the PSCs arecapable of proliferating in vitro for at least about 1 month or more,while maintaining pluripotency. In additional examples, the human PSCsare capable of proliferating in vitro for at least about 2, 3, or 4months or more, wherein the cell maintains its pluripotency. In otherembodiments, the PSCs are capable of proliferating in vitro for at leastabout 5, 6, or 7 months or more, wherein the PSCs maintain theirpluripotency. In another embodiment, the PSCs are capable ofproliferating in vitro for at least about 8 months or more, wherein thePSCs maintain their pluripotency. In a further embodiment, the PSCs arecapable of proliferating in vitro for at least about 9 months or more,wherein the PSCs maintain their pluripotency. The methods of obtainingand culturing these cells are provided in greater detail below.

In addition, the human pluripotent stem cells possess any one or more(including all) of the characteristic morphology: highnuclear/cytoplasmic ratios, prominent nucleoli, and compact colonyformation. The pluripotent cells can be characterized by the presence ofdiscrete cell surface markers or transcription factor expression thatincludes one or more (including all) of the following: OCT-4, SSEA-3,SSEA-4, TRA-1-60, and TRA-1-81. These cells are also characterized bymRNA expression of all or one or more (including all) of the following:POUSFI (OCT4), NANOG, SOX-2, TDGF, THY1, FGF4, TERT and LEFTYA. Thehuman pluripotent stem cells can also be characterized by the mRNAand/or protein expression of one or more (including all) of nuclearfactor (erythroid-derived 2)-like 3 (NFE2L3), nuclear receptor subfamily5, group A, member 2 (NR5A2), lymphocyte specific protein tyrosinekinase (LCK), V set domain containing T cell activation inhibitor 1(VTCNI), developmental pluripotency associated 4 (DPPA4), solute carrierfamily 12 (SLC12A1), C14orf115, myosin VIIA and rab interacting protein(MYRIP), alcohol dehydrogenase 4 (ADH4) and PR-domain containing 14(PRDM14) (See the GENECARD® website, GENBANK® and iHOP® web sites,available on the internet. Exemplary amino acid sequences and nucleicacid sequences are provided in GENBANK® as of May 8, 2013).

In addition to marker and transcription factor expression profiles, thehuman pluripotent stem cells can also maintain a normal diploidkaryotype. Both XX and XY cell lines can be derived. A normal karyotypeis one where all chromosomes normally present in a species are presentand have not been noticeably altered. Normal karyotype typically refersto the absence of chromosomal translocations, deletions or insertions.The normal karyotype is readily determined by any method known to one ofskill in the art, such as any banding technique, such as G-bandingand/or fluorescence in situ hybridization (FISH) for detectingtranslocation. The human pluripotent stem cells disclosed herein have akaryotype that is stable throughout in vitro culturing. In addition, thekaryotype remains stable even when the PSCs are cultured todifferentiate into organ-specific cells and used for treatment purposes,such as for transplantation.

The PSCs can be propagated as a self-renewing cell line as well asprovide a renewable source of MPSCs and other transplantable cells. PSCscan differentiate under appropriate conditions into the germ celllineage and viable gametes and three embryonic germ layers; mesoderm(for example, bone, cartilage, smooth muscle, striated muscle, andhematopoietic cells); endoderm (for example, liver, primitive gut andrespiratory epithelium); ectoderm (for example, neurons, glial cells,hair follicles and tooth buds). One of skill in the art is familiar withhow to assess the ability of PSCs to differentiate into cells of thethree germ layers. In one example, stem cells are implanted into ananimal model, such as a nude mouse, and the cells are allowed to growand form teratomas. After a suitable amount of time, the teratomas areremoved, sectioned and stained to ascertain the layers that have formed.If the cell is pluripotent, the resulting teratoma will contain tissuesfrom each of the three germ layers. In another example the PSCs arecultured in defined conditions in vitro to differentiate into specificcell types.

The human pluripotent stem cells disclosed herein are distinguished fromother human pluripotent stem cells described previously in that they aregenerated by transferring nuclear genetic material from the somatic cellof one individual (such as a patient) into a recipient cell, such as anoocyte, from another individual. That is, the stem cells derive theirnuclear genetic material from the subject of interest, while theenucleated recipient (or host) cell is from a different donor whichprovides mitochondrial DNA.

For example, the PSCs and MPSCs generated using the methods disclosedherein will have essentially identical nuclear genetic material to thesubject who is the source of the donor nuclear genetic material, and assuch autologous transplantation of differentiated cells derived from thestem cells should not induce immune rejection when transplanted backinto the donor.

The PSCs disclosed herein do not include human stem cells that have beengenerated using solely sperm-fertilized oocytes, and thus have an equalcontribution from two separate individuals (parents). Methods ofdetermining whether a stem cell has derived its nuclear genetic materialfrom one individual are readily known to one of skill in the art,including, but not limited to, microsatellite analysis. The humanpluripotent (or multipotent) stem cells disclosed herein havemitochondrial DNA from one individual and the nuclear DNA from a second,different individual. In one embodiment, the cells do not includemitochondrial DNA from the first individual of interest. Thus, in oneexample, the mitochondrial DNA and the nuclear DNA of the humanpluripotent stem cells (or multi potent stem cells) are from differentindividuals of the same species.

Disclosed herein is a purified preparation of human PSCs which (a) iscapable of being cultured for more than about one month in vitro; (b)maintains a normal karyotype; and (c) is capable of differentiating intogerm cells, ectoderm, mesoderm, and endoderm layers; wherein saidpluripotent stem cells are derived from an enucleated cell from a firstdonor and the nuclear genetic material from a second donor. The purifiedpreparation of human PSCs can possess one or more (including all) of thefollowing characteristics: (a) is capable of being cultured for morethan 4 months in vitro; (b) maintains a normal karyotype; (c) is capableof differentiating into germ cells, ectoderm, mesoderm, and endodermlayers; and (d) derives its nuclear genetic material from a singleindividual.

Compositions are disclosed that comprise one or more isolatedpluripotent human stem cells which possess one or more (including all)of the following characteristics: (a) are capable of being cultured formore than 1, 2, 3, 4, 5, or 6 months in vitro; (b) maintain a normalkaryotype while in culture; (c) are capable of differentiating into thegerm cell lineage, ectoderm, mesoderm, and endoderm layers; and (d)derive their nuclear genetic material from one individual. In someexamples, the pluripotent stem cells can be characterized by thepresence of mitochondrial DNA from an enucleated cell from a first donorand the nuclear genetic material from a second donor.

Multipotent stem cells produced from these human pluripotent stem cellsand stem cell lines are disclosed herein. These multipotent cells arenot pluripotent and give rise to cells of a specific lineage. In severalembodiments, the multipotent stem cells are capable of proliferating atleast 5, 6, 7, 8 or more cell divisions while retaining multipotency. Inadditional embodiments, the multipotent stem cells are capable of beingcultured for more than about 1, 2, 3, 4, 5, or 6 months in vitro. Thedisclosure also encompasses compositions, including, but not limited to,pharmaceutical compositions, comprising isolated multipotent cells whichhave been derived from one or more human pluripotent stem cells whichpossess one or more (including all) of the following characteristics:(a) are capable of being cultured for more than 1, 2, 3, 4, 5, or 6months in vitro; (b) maintains a normal karyotype while in culture; (c)are capable of differentiating into germ cells, ectoderm, mesoderm, andendoderm layers; and (d) derive their nuclear genetic material from oneindividual and their mitochondrial DNA from a second individual. In oneaspect, pluripotent stem cells are derived from an enucleated cell froma first human and the nuclear genetic material from a second human, andmultipotent stem cells are generated from these pluripotent cells.

Also provided herein are pluripotent human stem cell lines which possessone or more (including all) of the following characteristics: (a) arecapable of 4 or more cell divisions in vitro; (b) maintain a normalkaryotype while in culture; (c) are capable of differentiating into germcells, ectoderm, mesoderm, and endoderm layers; and (d) derive itsnuclear genetic material from one human donor and its mitochondrialgenetic material from another human donor.

Purified preparations of human pluripotent stem cells and multipotentcells are provided herein which have been generated using somatic cellnuclear transfer (SCNT). The successful generation of such cellsgenerally requires nuclear remodeling of the donor nucleus. The methodsdisclosed herein enable one of skill in the art to achieve success innuclear remodeling.

The indication that a cell is undergoing nuclear remodeling is generallyknown to one of skill in the art and involves events such as prematurechromatin condensation and nuclear envelope breakdown.

SCNT provides a way to produce isogenic cells of any cell type from adonor. Thus, provided are a preparation that comprises one or morepluripotent stem cells, or transplantable, cells that genetically matchto the nuclear donor cell. By genetically match, it is understood that a100% genetic match is not required but that that there is at least abouta 99.5% match. In some examples, the genetic match is at least about99%, at least about 98%, at least about 97%, at least about 96%, atleast about 95%, and at least about 94%. In other cases, the geneticmatch will be at least about 90% match. In one example, the geneticmatch is at one major histocompatibility (MHC) locus. In other examples,the match is at one or more MHC loci. In yet other examples, the geneticmatch is at 2, 3, 4, 5, 6 or more MHC loci. In still further examples,the genetic match is also at the minor histocompatibility loci.

Cell lines can also be derived from multipotent stem cells or othertransplantable cells derived from pluripotent stem cells. Also providedherein are preparations of transplantable cells derived from PSCs. Thesecells include, but are not limited to, neurons, cardiomyocytes,hematopoietic cells, keratinocytes, islet cells, mature gametes (spermor oocytes) or any other cell type, including any cell type of anorganism. In some embodiments, the purified preparation oftransplantable cells is incorporated into a pharmaceutical compositionor used in a method of treatment. The pharmaceutical composition canhave additives, carriers, media components or other component inaddition to the human transplantable cells.

Thus, compositions of human PSCs, MPSCs or transplantable cells and celllines derived from them are provided herein.

Methods

Methods of obtaining and culturing human pluripotent stem cells areprovided. The methods require the successful accomplishment of thefollowing: (a) effecting complete or essentially complete removal of thenuclear genetic material from a recipient cell which can be an oocyte toprovide an enucleated host cytoplast; (b) introduction of a nucleus froma somatic cell from the donor into the enucleated host cell cytoplast toform an SCNT embryo; and (c) that both (a) and (b) be carried out underconditions such that, upon nuclear remodeling of the introduced somaticcell nucleus in the cytoplasm of the host cell and the induction ofactivation, the resulting SCNT embryo exhibits the properties of asperm-fertilized embryo such that subsequent mitotic cell division leadsto the development of a blastocyst from which PSCs can be derived underculture conditions which typically sustain cultures of conventionalembryonic stem cell (ESC) lines derived from sperm-fertilized embryos,ultimately resulting in viable cultures of pluripotent stem cells.Generally the nuclear donor and the recipient cell (such as an oocyte)are from different individuals.

Any suitable cell can serve as a source for the enucleated host cellcytoplast provided that it permits sufficient nuclear reprogramming ofthe donor somatic cell nucleus. In general, the host cell is anunfertilized oocyte, but the donor can also be a pluripotent ESCcytoplast.

If oocytes are used as the cell to be enucleated, then one importantaspect of methodology is to use high quality oocytes. High qualityoocytes can be obtained by using protocols that stimulate the donor toproduce a number of viable oocytes. Examples of such stimulationprotocols are described in the Examples below. Another aspect that isimportant for ultimate success in developing pluripotent stem cells isthe method of harvesting. In one example, the oocytes can be harvestedusing methods known in the art, such as follicular aspiration, and thenseparated from contaminating blood cells. As an alternative, oocytes canbe generated from PSCs in vitro.

In one example, when human donors are stimulated to produce oocytes(such as hormonally) and these oocytes are harvested, the oocytes thatare collected can be in different phases. Some oocytes are in metaphaseI while other oocytes are in metaphase II. In such cases, the oocytesthat are in metaphase I can be put into culture until they reachmetaphase II and then used for enucleation to serve as the host cell.

Optionally, the oocytes that have been cultured to reach metaphase IIare combined with the oocytes that were already at metaphase II whenharvested for a pool of potential host cells. In other cases, only theoocytes that are in metaphase II from the harvest are used forenucleation. Any of these oocytes can be frozen for further use.

In some examples, the enucleation of the host cell is accomplished usinga technique that avoids an inhibition or down-regulation of maturationpromoting factor (MPF) or its activity. The enucleation of the host cellrefers to meiotic spindle removal. Maturation promoting factor or MPF isa heterodimeric protein comprising cyclin B and cyclin-dependent kinase1 (p34cdc2) that stimulates the mitotic and meiotic cell cycles. Withoutbeing bound by theory, MPF promotes the entrance into mitosis from theG2 phase by phosphorylating multiple proteins needed during mitosis.

The technique employed to enucleate the cell comprise using any imagingsystem that avoids reducing the MPF levels or activity. MPF activity orlevels can be determined by looking for biological effects that indicateactivation has occurred. Such effects include chromatin condensation andnuclear envelope breakdown. It is further contemplated that the SCNTtechniques useful in the method provided herein include not only thosethat directly impact MPF levels or activity, but also those thatindirectly affect MPF levels or activity.

In some examples, removal of nuclear genetic material (i.e.,enucleation) is accomplished without lowering the levels of maturationpromoting factor (MPF) or its activity. In one example, this means thatthe enucleation is accomplished without the use of UV-based enucleationprocedures such as Hoechst 33342 staining followed by UV visualization.One method that can be used in lieu of Hoechst 33342 is real timespindle imaging. In one example, the enucleation technique employs thereal time spindle imaging system such as the OOSIGHT™ Imaging System(CRI, Inc. Woburn, Mass.). This system utilizes a wavelength of 545 nmand has diffraction limited spatial resolution. The relay optics are0.65×. Generally the system includes a circular polarized interferencefilter with tunable liquid crystal polarizing filters However, anysystem that includes a liquid crystal tunable fiberoptic, a circularpolarizer/green interference fiber optic, and optionally a CCD camerawith software for image acquisition and analysis can be used for thispurpose. Generally, the system can merge polarized light imaging withsingle point analysis by quantifying magnitude and orientation ofbirefringence at each pixel in a field, in about real time. The spindleand the zona pellucida of an oocyte display an intrinsic property termed“birefringence” when trans-illuminated with polarized light, is aproperty that can be used for efficient visualization and alsoenucleation. The use of such a real time system permits non-invasivevisualization and the complete, or essentially complete, removal ofnuclear material from the oocyte or other cell. In one example, theentire mitotic spindle and its associated DNA from the host cell isremoved such that any potential for generating parthenotes is reduced oreliminated altogether.

In addition, exposure to caffeine, a protein phosphatase inhibitor(Kawahara et al, Reproduction 130, 351-357, (2005); Lee and Campbell,Bio Reprod 74, 691-698 (2006)) or the proteasome inhibitor, MG-132 (Zhouet al, Science 302, 1179 (2003)) increases the activity of MPF. MG-132can be utilized in the methods disclosed herein at concentrations, forexample, of about 0.1 to 10 μM, such as about 0.5 to about 10 μM, suchas about 0.5 to about 5 μM, such as about 1 to about 3 μM, such as about1 to about 2 μM. In some examples, 0.2, 2 or 5 μM MG-132 can beutilized. Caffeine can be used, for example at concentrations of about0.25 mM to about 25 mM, such as about 0.5 mM to 10 mM, such as 0.5 mM to2.5 mM, such as about 1.25 mM.

Any suitable somatic cell can be used as the source of the donornucleus. It will be appreciated by those skilled in the art that theselection of the somatic cell type from the donor to be the source ofthe nucleus for SCNT is not critical and can be selected from cells thatcan be removed in appropriate quantities from the donor withoutsignificant discomfort or risk. Exemplary somatic cells include, but arenot limited to keratinocytes, white blood cells, skin cells, and adiposecells. In one embodiment, the donor somatic cell nucleus can includemodified nucleic acids, such as nucleic acid (e.g., DNA) that includes arecombinant product. In one non-limiting example, the donor nucleus isobtained from a transgenic animal or an animal with an engineeredknock-out mutation. In a further example, the donor nucleic acidincludes heterologous DNA that encodes a protein product, such as adetectable marker, enzyme, or other protein. The donor nucleic acid canalso include other nucleic acids, such as ribozymes or antisense nucleicacid sequences. The heterologous nucleic acid can also be a regulatorysequence, such as a promoter, enhancer, insulator or repressor.Techniques for modifying nucleic acids are well known in the art, andinclude inserting a DNA that is synthetic or from another organism intothe donor nucleic acid, deleting one or more DNA sequences from thedonor, and introducing mutations, such as point mutations into the donornucleic acid. Methods and tools for manipulation of nucleic acids arewell known in the art, see for example Molecular Cloning: A LaboratoryManual, second edition (Sambrook et al, 1989) Cold Spring Harbor Press;Oligonucleotide Synthesis (M. J. Gait, ed., 1984); Animal Cell Culture(R. I. Freshney, ed., 1987); Methods in Enzymology (Academic Press,Inc.); Handbook of Experimental Immunology (D. M. Weir & C. C.Blackwell, eds.); Gene Transfer Vectors for Mammalian Cells (J. M.Miller & M. P. Calos, eds., 1987); Current Protocols in MolecularBiology (F. M. Ausubel et al, eds., 1987); PCR: The Polymerase ChainReaction, (Mullis et al., eds., 1994); Current Protocols in Immunology(J. E. Coligan et al., eds., 1991) Short Protocols in Molecular Biology(Wiley and Sons, 1999), Embryonic Stem Cells: A Practical Approach(Notaranni et al. eds., Oxford University Press 2006); and Essentials ofStem Cell Biology (R. Lanza, ed., Elsevier Academic Press 2006).

In another example, for either the enucleation step or the nucleartransfer step or both, the use of any suitable reagent that minimizescalcium fluxes in the donor cell immediately following nuclear transfercan be employed. Without being bound by theory, the reduction of calciumfluxes following nuclear transfer provides for more successful nuclearreprogramming. In one aspect, the avoidance of calcium fluxes oroscillation in the host cell allows for the MPF levels to be kept highand thus allow for more successful nuclear remodeling to occur.

In several examples, enucleation and/or nuclear transfer is performed incalcium (Ca²⁺)-free media. In additional examples, enucleation isperformed in magnesium (Mg²⁺) free media and calcium-free ions. Forexample, calcium-free phosphate buffered saline can be utilized. Thismedia is substantially free of calcium ions. In one embodiment, acalcium free medium contains less than about 10⁻⁶ M calcium cations

(Ca²⁺), such a media that contains less that as 10⁻⁷ M calcium cations,10⁻⁸M calcium cations, 10⁻⁹M calcium cations, or is substantially freeof calcium cations. Similarly, a magnesium-free medium contains lessthan about 10⁻⁶ M magnesium cations (Mg²⁺), such a media that containsless than about 10⁻⁷ M magnesium cations, 10⁻⁸ M magnesium cations, 10⁻⁹M magnesium cations, or is substantially free of magnesium cations. Theselection of the appropriate media or other reagents that will, forexample, chelate extracellular calcium and/or magnesium, such asethylene glycol tetraacetic acid (EGTA) or ethylenediamine tetraaceticacid (EDTA), do not have added calcium and/or magnesium ions, orotherwise reduce the calcium fluxes during these manipulations are knownin the art. Exemplary media are described in the Examples below. Thesemedia and reagents are commercially available, and suitable media can beroutinely produced in the laboratory.

The amount of time required after introduction of the donor nucleus tothe recipient cell for a premature condensed chromosome and spindle toform can vary from cell type to cell type and/or from species tospecies. In order to allow sufficient time for the premature condensedchromosome and spindle to form, the cell can require culturing for fromabout 0.5 hours to about 10 hours, from about 1 hour to about 8 hours,from about 1.25 hours to about 6 hours, from about 1.5 hours to about 4hours, from about 1.75 hours to about 3 hours, or about 2 hours afterintroduction of the donor nucleus to the recipient or host cell.

Accordingly, methods are provided for producing a human pluripotent stemcell comprising the steps of: (a) enucleating a human oocyte by using anon-UV-based spindle imaging system such that a sufficient amount of thenucleus is removed such that parthenogenesis cannot occur; and (b)introducing the nucleus of a human somatic cell into the enucleatedcell, wherein the enucleation and insertion steps occur in the presenceof a protein phosphatase inhibitor such as caffeine or MG-132, andwherein the resulting SCNT embryo is activated using an electroporationpulse.

Following introduction of the donor somatic cell nucleus into theenucleated recipient cell, the cell is cultured in vitro. Methods ofculturing human blastocyts or pluripotent stem cells are well-known inthe art. Any cell culture media that can support the growth anddifferentiation of human embryonic stem cells can be used. In someembodiments, the pluripotent stem cells are cultured on a feeder layer,such as of murine or human embryonic fibroblasts. However, the feederlayer can include any cell that supports the growth of ESCs. Thisapproach makes for a completely autologous culturing system, therebyeliminating the risk of cross-species contamination. For therapeuticuse, the culturing methods can be xeno-free (no xenogeneic cells orcomponents) and can also avoid use of serum (such as fetal bovine serum,FBS) in the culture media.

Human pluripotent cells can be isolated and subsequently cultured in “ESmedium,” which supports the growth of embryonic stem cells. For example,ES medium comprises 80% Dulbecco's modified Eagle's medium (DMEM; nopyruvate, high glucose formulation, Gibco BRL), with 20% fetal bovineserum (FBS; Hyclone), 0.1 mM B mercaptoethanol (Sigma), 1% non-essentialamino acid stock (Gibco BRL).

In one example, an oocyte is enucleated using the methods disclosedabove, and a somatic cell nucleus is inserted into the enucleatedoocyte, as described herein. The resultant cell is then cultured inmedium, such as but not limited to protein free HECM-9 medium andcultured at 37° C. in about 5-6% CO₂ until use. These cultures can bemaintained under paraffin oil. Once the SCNT embryo reaches about the 2cell stage or beyond, such as the 4, 8 or 16 cell stage, the cells canbe transferred for further culture. In one embodiment, these SCNTembryos are cultured to the blastocyst stage in a culture medium, suchas, but not limited to, HECM-9 medium.

In some embodiments, the zonae pellucidae of selected expandedblastocysts are removed by brief exposure (45-60 seconds) to 0.5%pronase in TH3 medium. In some embodiments an ICM can be isolated fromtrophectoderm cells by immunosurgery, where zona-free blastocysts areexposed to rabbit anti-rhesus spleen serum for about 30 minutes at about37° C. After extensive washing (such as using TH3 medium), embryos areincubated in guinea pig complement reconstituted with HECM-9 (1:2, v/v)for about an additional 30 minutes at about 37° C. Partially lysedtrophectodermal cells are mechanically dispersed by gentle pipetting,such as with a small bore pipette (for example, about a 125 μl in innerdiameter; Stripper pipette, Midatlantic Diagnostics Inc., Marlton, N.J.)followed by the rinsing of ICMs three times, such as with TH3 medium.Isolated ICMs are plated onto a solid substrate, such as onto Nunc4-well dishes containing mitotically-inactivated feeder layersconsisting of mouse embryonic fibroblasts (mEFs) and cultured, such asin DMEM/F12 medium (Invitrogen) with glucose and without sodium pyruvatesupplemented with 1% nonessential amino acids (Invitrogen), 2 mML-glutamine (Invitrogen), 0.1 mM β-mercaptoethanol and 15% FBS andmaintained at about 37° C., about 3% CO₂, about 5% O₂ and about 92% N₂conditions. Alternatively, whole, intact blastocysts can be directlyplated onto mEFs for ESC isolation.

After about 1 to about 7 days, cells, such as blastocysts or ICMs thatattached to the feeder layer and initiated outgrowth can be dissociatedinto small cell clumps, such as manual dissociation with a microscalpel,and re-plated onto a new substrate, such as new embryonic fibroblasts(mEFs). After the first passage, colonies with embryonic stem cell (ESC)like morphology are selected for further propagation, characterizationand low temperature storage. Generally, ESC morphology is compactcolonies having a high nucleus to cytoplasm ratio, prominent nucleoli,sharp edges and flat colonies. In some examples, the medium is changeddaily and ESC colonies are split about every 5-7 days manually or bydisaggregation in collagenase IV, (for example, about 1 mg/ml, at about37° C. for about 2-3 minutes; Invitrogen) and replating collected cellsonto dishes with fresh feeder layers. Cultures are maintained at about37° C., about 3% CO₂, about 5% O₂ and about 92% N₂. In anotheralternative, serum-free media is used.

PSCs can then be isolated, and PSCs can be maintained in vitro usingstandard procedures. In one example, human PSCs are isolated on aconfluent layer of fibroblast in the presence of ESC medium. In oneexample, to produce a feeder layer, xenogeneic embryonic fibroblasts areobtained from 14-16 day old fetuses from outbred mice (such as CF1,available from SASCO), but other strains can be used as an alternative.Alternatively, human fibroblasts obtained from adult skin or cellsobtained from TSC-derived fibroblasts can be employed. In anotherembodiment, tissue culture dishes treated with about 0.1% gelatin (typeI; Sigma) can be utilized. Unlike mouse PSC cells, human PSC (hPSC)cells do not express the stage-specific embryonic antigen SSEA-1, butexpress SSEA-4, which is another glycolipid cell surface antigenrecognized by a specific monoclonal antibody (see, for example, Amit etal, Devel Biol 227, 271-278, (2000)).

ICM-dissociated cells can be plated on feeder layers in fresh medium,and observed for colony formation. Colonies demonstrating ESC morphologyare individually selected, and split again as described above. ResultingPSCs are then routinely split by mechanical methods every six days asthe cultures become dense. Early passage cells are also frozen andstored in liquid nitrogen.

PSCs as well as transplantable cells can be produced and can bekaryotyped with, for example, a standard G-banding technique (such as bythe Cytogenetics Laboratory of the University of Wisconsin State HygieneLaboratory, which provides routine karyotyping services) and compared topublished human karyotypes.

In other embodiments, immunosurgical isolation of the ICM is notutilized. Thus, the blastocysts are cultured directly, without the useof any immunosurgical techniques. Culture conditions described above canalso be used for the culture of PSCs from blastocysts. Conditions forculturing human totipotent stem cells obtained by conventional protocolsfrom fertilized oocytes to the blastocyst have been described (seeBongso et al, Hum Reprod 4, 706-713, (1989)). In some embodiments,co-culturing of human SCNT embryos with human oviductal cells results inthe production of high quality blastocysts. Human ICM from blastocystsgrown in cellular coculture or in media that eliminates the feeder celllayer requirement allows isolation of human PSCs with the sameprocedures described above.

Uses of Human Pluripotent Stem Cells

Also provided herein are therapeutic compositions comprised oftransplantable cells which have been derived (produced) from PSCs in aformulation suitable for administration to a human subject. In oneexample, that human subject is the source of the somatic nucleus. Thetherapeutic compositions include multipotent cells, lineage-specificstem cells, as well as partly or fully differentiated cells derived fromthe PSCs provided herein.

The cells can be matched at one or more loci of the majorhistocompatibility complex (MHC). In one example, there is a completematch at every MHC loci. In another example, the PSCs are made by thetransfer of a nucleus from a somatic cell of the subject into anenucleated oocyte from a second individual as described herein. Atherapeutically effective amount of pluripotent or multipotent cells canthen be used to treat the subject.

Methods for treating disease are provided that comprise transplantingPSCs or cells derived from PSCs in a human subject afflicted with adisease characterized by damaged or degenerative somatic cells. Suchcells can be multipotent cells or any other type of transplantablecells.

The human PSCs described herein are useful for the generation of cellsof desired cell types. In some embodiments, the PSCs are used to derivemesenchymal, neural, and/or hematopoietic stem cells. In otherembodiments, the PSCs are used to generate cells, including but notlimited to, pancreatic, liver, bone, epithelial, endothelial, tendons,cartilage, and muscle cells, and their progenitor cells. Thus,transplantable cells derived from PSCs can be administered to anindividual in need of one or more cell types to treat a disease,disorder, or condition. Examples of diseases, disorders, or conditionsthat can be treated or prevented include neurological, endocrine,structural, skeletal, vascular, urinary, digestive, integumentary,blood, immune, auto-immune, inflammatory, kidney, bladder,cardiovascular, cancer, circulatory, hematopoietic, metabolic,reproductive and muscular diseases, disorders and conditions. In someembodiments, a hematopoietic stem cell derived from human PSCs is usedto treat cancer. In some embodiments, these cells are used forreconstructive applications, such as for repairing or replacing tissuesor organs.

The PSCs described herein can be used to generate multipotent stem cellsor transplantable cells. In one example, the transplantable cells aremesenchymal stem cells. Mesenchymal stem cells give rise to a very largenumber of distinct tissues (Caplan, J Orth Res 641-650 (1991)).Mesenchymal stem cells capable of differentiating into bone, muscles,tendons, adipose tissue, stromal cells and cartilage have also beenisolated from marrow. U.S. Pat. No. 5,226,914 describes an exemplarymethod of isolating mesenchymal stem cells from bone marrow. In otherexamples, epithelial progenitor cells or keratinocytes can be generatedfor use in treating conditions of the skin and the lining of the gut(Rheinwald, Meth Cell Bio 21A, 229 (1980)). The cells can also be usedto produce liver precursor cells (see PCT Publication No. WO 94/08598)or kidney precursor cells (see Karp et al, Dev Biol 91, 5286-5290(1994)). The cells can also be used to produce inner ear precursor cells(see Li et al, Trends Mol Med 10, 309 (2004)).

The transplantable cells can also be neuronal cells. The volume of acell suspension, such as a neuronal cell suspension, administered to asubject will vary depending on the site of implantation, treatment goaland amount of cells in solution. Typically the amount of cellsadministered to a subject will be a therapeutically effective amount.For example, where the treatment is for Parkinson's disease,transplantation of a therapeutically effective amount of cells willtypically produce a reduction in the amount and/or severity of thesymptoms associated with that disorder, e.g., rigidity, akinesia andgait disorder. In one example, a severe Parkinson's patient needs atleast about 100,000 surviving dopamine cells per grafted site to have asubstantial beneficial effect from the transplantation. As cell survivalis low in brain tissue transplantation in general (5-10%) at least 1million cells are administered, such as from about 1 million to about 4million dopaminergic neurons are transplanted. In one embodiment, thecells are administered to the subject's brain. The cells can beimplanted within the parenchyma of the brain, in the space containingcerebrospinal fluids, such as the sub-arachnoid space or ventricles, orextaneurally. Thus, in one example, the cells are transplanted toregions of the subject which are not within the central nervous systemor peripheral nervous system, such as the celiac ganglion or sciaticnerve. In another embodiment, the cells are transplanted into thecentral nervous system, which includes all structures within the duramater. Those of skill in the art are familiar with techniques foradministering cells to the brain of a subject.

Human PSCs produced using the methods disclosed herein are capable ofcontributing to the germ line. Thus, somatic cells from a subject ofinterest can be used to produce ES cells which subsequently can bedifferentiated into oocytes or sperm. These oocytes or sperm can then beused for fertilization, allowing an infertile subject to producechildren that are genetically related to the subject. In addition, EScell-derived eggs are of use in research. For example, these eggs can inturn be used to make SCNT-derived ES cells. This availability of theseoocytes can reduce the use of donated human eggs for research.

Cells produced by the methods disclosed herein, such as PSC are also ofuse for testing agents of interest, such as to determine if an agentaffects differentiation or cell proliferation. For example, PSCs arecontacted with the agent, and the ability of the cells to differentiateor proliferate is assessed in the presence and the absence of the agent.Thus, cells produced by the methods disclosed herein can also be used into screen pharmaceutical agents to select for agents that affectspecific human cell types, such as agents that affect neuronal cells.Cells produced by the methods disclosed herein can also be used toscreen test compounds to select those that affect differentiation. Atest compound can be any compound of interest, including chemicalcompounds, small molecules, polypeptides or other biological agents (forexample antibodies or cytokines). In several examples, a panel ofpotential agents is screened, such as a panel of cytokines or growthfactors is screened.

EXAMPLES

The following examples are illustrative of disclosed methods. In lightof this disclosure, those of skill in the art will recognize thatvariations of these examples and other examples of the disclosed methodwould be possible without undue experimentation.

Example 1—Overview

Reprogramming of somatic cells to pluripotent embryonic stem cells(ESCs) by somatic cell nuclear transfer (SCNT) was long hoped togenerate patient-matched nuclear transfer derived-ESC (NT-ESCs) to studydisease mechanisms and to develop therapies. Until now, all attempts toproduce human NT-ESCs have failed, largely due to early embryonic arrestof SCNT embryos. Disclosed herein is the identification of prematureexit from meiosis in human oocytes and suboptimal activation as keyfactors responsible for embryonic arrest. Disclosed herein are optimizedSCNT methods designed to overcome these defects and that allow, for thefirst time, derivation of human NT-ESCs. NT-ESCs displayed normaldiploid karyotypes and inherited their nuclear genome exclusively fromparental somatic cells. Gene expression and differentiation profiles inhuman NT-ESCs were similar to genuine embryo derived ESCs suggestingefficient conversion of somatic cells to pluripotency.

The main roadblock to producing human NT-ESCs is the embryonic arrest ofhuman SCNT embryos prior to the development of stable NT-ESCs.Typically, SCNT embryos fail to progress beyond the 8-cell stage,presumably due to inability to activate critical embryonic genes fromthe somatic nucleus (Egli D et al, Nature Comm 2, 488 (2011) and NoggleS et al, Nature 478, 70-75 (2011)). In those few cases describing SCNTembryos reaching the blastocyst stage, such embryos failed to producestable ESCs (Fan Y et al, Stem Cells Dev 20, 1951-1959 (2011) and FrenchA J et al, Stem Cells 26, 485-493 (2008).

While the underlying cause of this early developmental arrest remainsunclear, these studies mechanically applied SCNT protocols developed forother species for human oocytes. It has been previously demonstratedthat, to be effective, SCNT procedures must be adapted to primates.Reprogramming of rhesus macaque adult skin fibroblasts into NT-ESCs wasachieved (Byrne J A et al, Nature 450, 497-502 (2007) and Sparman M etal, Stem Cells 27, 1255-1264 (2009)).

Removal of a human oocyte's nuclear genetic material (chromosomes)negatively impacts the ability of the cytoplast to induce reprogramming(Noggle et al, 2011 supra). However, when a somatic cell nucleus wastransplanted into an intact oocyte with a full set of chromosomes, theresulting polyploid embryos were able to overcome the developmentalblock and produce ESCs.

It was also observed that the meiotic arrest in human MII oocytes isunstable and can be perturbed by mechanical manipulations (Tachibana Met al, Nature 493, 627-631 (2013)). Additionally, retention of meiosisspecific activity in a cytoplast is critical for nuclear remodelingafter the transplantation of an interphase somatic cell nucleus(Mitalipov S M et al, Hum Reprod 22, 2232-2242 (2007)). Nuclearremodeling is positively correlated with further development of SCNTembryos after activation. Therefore, modifications in oocyte enucleationand donor cell introduction that retain meiosis factors in humancytoplasts were systematically evaluated.

It is disclosed herein that routine artificial activation treatments areinsufficient to support subsequent human SCNT development and thatalterations in SCNT significantly improve blastocyst formation by humanSCNT embryos. Several human NT-ESC lines were derived from theseembryos. These NT-ESC lines were validated by their nuclear DNA beingidentical to the nuclear donor somatic cells but with theirmitochondrial DNA being identical to that of the recipient oocytes.Finally, extensive pluripotency assays were performed on the derivedhuman NT-ESCs and their complete reprogramming was verified.

Example 2—SCNT Protocol Optimizations in a Nonhuman Primate Model

Human MII oocytes are subject to premature activation induced by removaland re-introduction of meiotic spindles (Tachibana et al, 2013 supra). Alarge portion of oocytes subjected to human spindle transfer (ST)underwent spontaneous resumption and exited from meiosis beforefertilization, suggesting that mechanical manipulations cause a declinein meiotic kinase activities. In addition, nuclear envelope breakdown(NEBD) and premature chromosome condensation (PCC), which occurimmediately after introduction of an interphase somatic cell nucleus,for improved SCNT development (Mitalipov et al, 2007 supra).

It was reasoned that the developmental arrest of human SCNT embryos andtheir failure to produce NT-ESCs could be due to lack of or incompleteNEBD and PCC. Therefore, new nuclear transfer protocols that minimizepremature activation were necessary.

Cell fusion induced by electroporation was shown to deliver a precociousactivation stimulus to the cytoplast which resulted in exit from meiosis(Tachibana M et al, Nature 461, 367-372 (2009). An earlier-describedspindle transfer protocol replaced electrofusion with hemagglutinatingvirus of Japan (HVJ-E). Use of HVJ-E was critical to maintain cytoplastsin meiosis (Tachibana et al, 2009 supra). This HVJ-E-based cell fusionwas then used to develop rhesus macaque SCNT embryos.

Fusion rates were 100% using either electrofusion or HVJ-E suggestingthat introduction of donor cell nuclei can be efficiently used for bothapproaches. Interphase somatic nuclei introduced by electrofusionmaintained intact nuclear membrane as detected by Lamin B staining withno detectable premature chromosome condensation. (FIG. 1A). In contrast,nuclei of HVJ-E fused cells underwent rapid NEBD followed by PCC within30 minutes after fusion (FIG. 1A). Efficient NEBD and PCC wereassociated with formation of spindle-like structures easily detectableby non-invasive examination using a polarized microscope. These resultsare in agreement with premature activation and decline in the activityof meiotic factors caused by electroporation. In an unexpected result,however, SCNT embryos generated by HVJ-E fusion failed to progressbeyond the compact morula stage while a small portion of control SCNTembryos produced by electrofusion reached the blastocyst stage (FIGS. 1Band C).

These results suggested that electrofusion would be beneficial for SCNTreprogramming and can act as an additional activation stimulus. As aresult, HVJ-E fused SCNT embryos were exposed to the electroporationprior to standard lononnycin/DMAP activation treatment. Indeed, thistreatment produced SCNT embryos capable of reaching the blastocyst stageat a rate similar to controls (FIGS. 1B and C). Unexpectedly, the SCNTblastocyst formation rate was unaffected even when exposure to lonomycinwas omitted and SCNT embryos were activated with electroporationfollowed by DMAP treatment (FIG. 8). Together these data indicate thatwhile electroporation stimulus is not required for cell fusion, it isimportant for proper cytoplast activation following SCNT.

Histone deacetylase inhibitors, such as trichostatin A (Chan et al, JPedodontics 7, 18-35 (1982)), have been associated with improved SCNTreprogramming in several mammalian species (Ding X et al, Theriogenology70, 622-630 (2008); Kishigami S et al, Biochem Biophys Res Comm 340183-189 (2006); and Li J et al, Theriogenology 70, 800-808 (2008)).Enhanced development of monkey SCNT embryos to blastocysts was observedwhen the embryos are treated with 37.5 nM TSA (from 4% to 18%) (SparmanM et al, Stem Cells 27, 1255-1264 (2010)).

However, the quality of such blastocysts and their potential to giverise to stable ESCs remained unknown until this current disclosure. Atotal of 16 monkey SCNT blastocysts produced with TSA treatment wereplated on mitotically inactivated mouse embryonic fibroblast (mEF)feeders. None of these blastocysts produced NT-ESC lines (Table 1).Lower TSA concentrations as well as shorter exposure times to TSA had noeffect on monkey SCNT blastocyst development and ESC isolation. Reducingthe TSA concentration to 10 nM or shortening the TSA exposure time from24 h to 12 h did not affect blastocyst rates (Table 1). Notably, onlySCNT blastocysts produced with 10 nM TSA supported derivation of stablemonkey NT-ESC lines (Table 2).

TABLE 1 Monkey SCNT embryo development after treatment with trichostatinA (TSA) TSA concentration fused 8-cell Blastocysts and time rep N (%) PN(%) (%) CM (%) (%) 37.5 nM for 24 h 39 511 503 (98.4) 498 (99.0) 418(90.3) 107 (23.1) 85 (18.4)   10 nM for 24 h 10 108 104 (95.4) 104(100)  100 (97.1)  33 (32.0) 25 (24.3)   10 nM for 12 h 37 571 567(99.3) 535 (94.4) 494 (93.7) 147 (27.9) 99 (18.8)   5 nM for 12 h 16 212210 (99.1) 207 (98.6) 192 (92.8)  58 (26.0) 30 (14.5)

TABLE 2 Monkey NT-ESC isolation after treatment with TSA TSAConcentration TSA duration # Plated blastocyst # NT-ESCs (%) 37.5 nM 24h 16 0   10 nM 24 h 4 0 12 h 23 3 (13%)   5 nM 12 h 7 0

Example 3—Producing Human SCNT Blastocysts and NT-ESC Lines

This example describes the production of human SCNT blastocysts andNT-ESC lines. Human MII oocytes were collected from healthy volunteers(age 23-33) and subjected to the SCNT protocol that produced bestresults in a nonhuman primate model. Oocytes were retrieved followingstandard ovarian stimulation protocols and transvaginal follicularaspirations. Human dermal fibroblasts of fetal origin (HDF-f)synchronized in G0/G1 cell cycle phase were used as nuclear donors (FIG.2A). Removal of spindles and HVJ-E-assisted donor cell fusion wascarried out within 60 min after oocyte retrievals.

Most oocytes (95.2%: 60/63) survived MII spindle removal conducted underpolarized microscopy (Oosight™) (Byrne et al, (2007) supra; Sparman etal, (2009) supra) and nuclei from donor fibroblasts were introducedusing the HVJ-E fusion described above. Efficiency of fusion was 100%.Immediately after confirmation of fusion, oocytes were activated withelectroporation/DMAP (4 h) and exposed to 10 nM TSA for 12 hours. Themajority of human SCNT embryos (81.7%, 49/60), formed one or twopronuclei at the time of removal of TSA. A slightly higher portion ofembryos cleaved (86.7% 52/60) suggesting that some SCNT embryos did notexhibit visible pronuclei at the time of examination (FIG. 3A). Themajority of cleaved embryos developed to the 8-cell stage (61.5%,32/52), but fewer still progressed to the compact molura (CM) (13.5%,7/52) and blastocyst (11.5%, 6/52) stages (FIG. 3A).

Activation of embryonic genes and transcription from the transplantedsomatic cell nucleus are required for development of SCNT embryos beyondthe 8-cell stage (Egli et al, (2011) supra; Noggle et al, (2011) supra).Therefore, these results suggest that these methods successfullyreprogram of human somatic cells to the embryonic state. However, humanSCNT blastocysts exhibited poorly organized trophectoderm and small orundetectable inner cell masses (ICMs). In addition, largeblastomere-like cells were excluded into a civility of SCNT blastocysts(FIG. 2B). Six of these SCNT blastocysts were plated onto a feeder layerto examine their ability to support ESC derivation. Four of theblastocysts attached to the mEFs feeder cells, but only one displayed anoutgrowth that was further passaged. The further passaging failed toproduce stable ESC-like cells (FIG. 3B).

Clearly, further optimization of human SCNT protocols was needed toproduce viable NT-ESCs. Somatic nuclei were introduced into intact humanMII oocytes and their birefringence properties assessed using apolarized microscope. All somatic nuclei introduced into MII oocytesefficiently formed spindle-like structures that were visible within 30min after fusion (17/17) (FIG. 2C). However, spindle formation was notobserved when the somatic cell nuclei were fused with enucleated humanoocytes (0/3). These observations are consistent with other recentobservations that human MII oocytes undergo premature activation causedby enucleation (Tachibana et al, 2013 supra).

Exposure of monkey oocytes to caffeine, a protein phosphatase inhibitor,was effective in protecting the cytoplast from premature activation andimproved the development of SCNT embryos (Mitalipov et al, 2007 supra).Therefore, human oocytes were maintained in 1.25 mM caffeine duringenucleation and somatic cell fusion. As expected, somatic cell nucleiintroduced into oocyte cytoplasts under these conditions efficientlyformed spindle-like structures detectable under birefringence microscope(83.3%, 10/12) (FIG. 2D). More importantly, blastocyst development ofcaffeine treated embryos was also notably enhanced (23.5%) compared tostandard SCNT group (FIG. 3A). Human SCNT blastocysts in this groupcontained visible, prominent ICMs similar to that observed for IVFembryos (FIG. 2E).

Remarkably, when eight SCNT blastocysts produced with caffeine wereutilized for ESCs isolation, all attached to mEFs and 4 formed an ICMoutgrowth (FIG. 3B). All four ICM outgrowths gave rise to ESC-likecolonies upon manual splitting onto fresh mEF plates (FIG. 2F).Subsequent passaging resulted in efficient propagation of stable ESCcolonies with typical morphology and growth characteristics. Thissurprisingly high ESC derivation rate was similar to that reported inour previous study with human IVF-derived blastocysts (50%) and was evenhigher than in manipulated ST embryos (38%) (FIG. 3B) (Tachibana et al,2013 supra).

Collectively, our findings indicate that protocols perfected in a NHPmodel support blastocyst development for human SCNT embryos. However,poor quality of human SCNT blastocysts precluded ESC isolation.Incorporation of caffeine during enucleation and fusion, to counterspontaneous activation of human MII oocytes, improved blastocystdevelopment and supported derivation of ESCs.

Example 4—Reproducibility of Human SCNT Results

All 4 human NT-ESC lines produced by the disclosed method were derivedfrom oocytes retrieved from one particular egg donor. Eight mature MIIoocytes were recovered from this donor after a single stimulation cycleand used for SCNT. Using the disclosed methods, 5 blastocysts wereproduced (62.5%) that gave rise to 4 NT-ESC lines (80%) (FIG. 9). Inaddition, all four cell lines were derived using fetal dermalfibroblasts as nuclear donors. In the context of generatingpatient-specific pluripotent stem cells, the therapeutic potential ofSCNT depends on reproducibility of results with various patient-derivedsomatic cells and different oocyte donors.

A skin fibroblast culture was obtained from a patient with Leighsyndrome. A total of 15 and 5 MII oocytes were collected from twounrelated egg donors (donors #11 and #12, respectively). The disclosedSCNT methods were then performed using nuclei from the skin fibroblasts.All oocytes survived enucleation and successfully fused with donorcells. Following activation and culture, 4 (27%, 4/15) and 3 (60%, 3/5)blastocysts were produced from the each egg donor, respectively (FIG.4A). After plating on mEFs and manual passaging, two stable NT-ESC lineswere established, one from the each egg cohort (FIG. 4B). Thus, theseoutcomes confirm the reproducibility and efficacy of the disclosed SCNTprotocols with another nuclear donor cells and different cohort of humanoocytes.

Example 5—Retrospective Analysis of Factors Affecting the Success ofHuman SCNT

Although SCNT manipulations and treatments were strictly controlled, thequality and quantity of human oocytes retrieved from different eggdonors varied significantly. An excessive number of oocytes retrievedfrom a cycle is generally associated with poor clinical IVF outcomes(Pellicer A et al, Hum Reproduction 4, 536-540 (1989); Santos M A et al,Reproduction 139, 23-34 (2010); and van der Gaast M H et al, ReprodBiomed Online 13, 476-480 (2006)).

A retrospective analysis of ovarian stimulation procedures was conductedin order to determine the effect of the number of oocytes retrieved percycle on human SCNT embryo development and NT-ESC derivation outcomes.Oocyte donation cycles were divided into three groups based on the rangeof collected mature MII oocytes—10 or fewer oocytes per cycle (5donors), between 11 to 15 oocytes (2 donors) and more than 16 oocytesper cycle (3 donors). While survival after enucleation, fusion,pronuclear formation and cleavage of SCNT embryos were similar betweenthese groups, more embryos derived from the donors producing ≧16 MIIoocytes/cycle arrested after the 8-cell stage than the other two groups(FIG. 5A). In addition, the quality of SCNT blastocysts also negativelycorrelated with the number of collected oocytes per cycle. While fiveNT-ESC lines were derived from donors producing ≦10 oocytes/cycle, onlyone line was produced from donors producing 11-15 oocytes per cycle andno cell line was established from cycles with 16 oocytes (FIG. 5B). Thepeak estradiol (E2) level measured in blood of egg donors prior to hCGpriming positively correlated with the subsequent yield of oocytes (FIG.10). Thus, these observations imply that the higher the number ofoocytes collected, the worse the oocyte quality and reprogrammingability in the context of SCNT.

Optimal stimulation protocols giving the best chance of producingoocytes capable of producing NT-ESCs using SCNT were sought. The impactof GnRH agonists and antagonists used to suppress the pituitary functionof egg donors were first assessed. Prior to stimulations, theanti-mullerian hormone (AMH) level and antral follicle counts (AFC) weremeasured for each individual egg donor (Table S3). Donors with higherAMH and AFC profiles are associated with high ovarian reserve andreceived the GnRH agonist Lupron® (4 cycles) while the remaining donorswere provided with the GnRH antagonist (ganirelix, 6 cycles) (Table 3).

TABLE 3 Clinical values for different pituitary suppression regimengroups GnRH antagonist GnRH agonist # Cycles 6 4 # oocytes 11.7 ± 5.6 20.5 ± 11.9 NS Age  29 ± 2.5 24.3 ± 1.3  P < 0.05 AMH (ng/ml) 2.8 ± 0.54.2 ± 1.2 P < 0.05 AFC 23.1 ± 7.2  33.3 ± 5.4  P < 0.05 FSH dosage (IU)958.3 ± 241.7   950 ± 253.3 NS # hMG samples 8.5 ± 1.6 8.8 ± 0.9 NSStimulation days 8.7 ± 1.6   9 ± 0.8 NS Peak E2 2568.2 ± 806.1    2709 ±1597.3 NS

The average number of MII oocytes (mean±SD) collected per cycle was notstatistically different between the GnRH antagonist and GnRH agonisttreated groups (11.7±5.6 and 20.5±11.9, respectively). However, SCNTembryo development beyond the 8-cell stage was impaired in oocytesproduced with GnRH agonist treatment (FIG. 5C). Moreover, all six NT-ESClines were derived from oocytes collected from donors treated with GnRHantagonist (FIG. 5D). Based on these observations, it is reasonable toconclude that pituitary suppression with GnRH agonists during ovarianstimulations can result in production of oocytes with diminishedquality, incompatible with SCNT blastocyst development and ESCisolation.

Pronuclear formation was also assessed for use as a predictive markerfor SCNT outcomes. The majority of SCNT embryos formed a singlepronucleus the day next after nuclear transfer (56%, 68/122), while asmaller portion (20%, 24/122) displayed 2 pronuclei (FIG. 11). Asindicated above, pronuclear formation was not observed in a portion of1-cell SCNT embryos (20%, 24/122), or they already progressed to the2-cell stage by the time of the pronuclear check (FIG. 11). Afterseparate culture, it was determined that cleavage and earlypreimplantation development was similar among these groups. While therate of blastocyst formation was higher in SCNT embryos with 2 pronuclei(39%), stable NT-ESC lines were produced from all four types of embryos(FIG. 11). Although small numbers of SCNT embryos were analyzed, it isreasonable to conclude that pronuclear formation does not directlycorrelate with NT-ESC derivation.

Example 6—Analysis of Human NT-ESCs

To determine the SCNT origin and to define the degree of reprogrammingthe four NT-ESC lines (designated as hESO-NT1, 2, 3, and 4) derived fromHDF-f fetal fibroblasts, were expanded and extensively analyzed.Initially, microsatellite typing using 23 markers mapping 22 humanautosomal loci and one X-linked locus for nuclear genome genotyping(Tachibana et al, 2013 supra) was used. The results undoubtedly matchedall 4 NT-ESC lines to the donor fetal fibroblasts with no detectablecontribution of alleles from oocytes (FIG. 6A and Table 4). The definingfeature of SCNT is that the mitochondrial genome (mtDNA) in SCNT embryosand NT-ESCs is largely contributed by the oocyte. As expected, analysisof mtDNA sequence differences within the displacement loop (D-loop)containing the hypervariable segment (HSV) confirmed that NT-ESC linesinherited mainly oocyte mtDNA (FIG. 6B). During fusion of cytoplastswith nuclear donor fibroblasts, a small amount of somatic mtDNA isco-transferred into SCNT embryos that can result in heteroplasmy inNT-ESCs. Sensitive ARMS-qPCR (amplification refractory mutationsystem-quantitative polymerase chain reaction) was used and detected alow level of somatic mtDNA contribution in all four NT-ESC lines(3.4±1.7%; range 1.2-4.9%) (Table S5). This carryover was higher thanthat seen in spindle transfer-ESC lines (0.6±0.9%) derived after spindletransfer between oocytes (Tachibana et al, 2013 supra). Cytogeneticanalysis by G-banding analysis indicated that all 4 NT-ESC lines containa normal euploid female karyotype (46XX) with no numerical or structuralabnormalities (FIG. 6C and Table 5).

To assess pluripotency in NT-ESC lines, expression of common markerswere assessed by immunocytochemistry (ICC) and compared to the twoIVF-derived ESC lines (hESO-7 and -8). Note that the control ESC linesand the four NT-ESC lines were established from the oocytes donated bythe same donor, thus carried identical mtDNA (Tachibana et al, 2013supra). Similar to controls, all NT-ESC lines expressed OCT-4, NANOG,SOX2, SSEA-4, TRA-1-60 and TRA-1-81 (FIG. 6D and Table 6). When injectedinto immunodeficient SCID mice, all NT-ESC lines produced tumorsconsisting of tissue and cell types representing all three germ layers(FIG. 6E). An in vitro differentiation assay demonstrated efficientformation in embryoid bodies in suspension culture that after attachmentformed spontaneously contracting cardiomyocytes).

TABLE 4 Microsatellite analysis of human NT-ESC lines Oocyte hESO- hESO-hESO- hESO- Sample HDF-f donor NT1 NT2 NT3 NT4 Sex F F F F F F AME XX XXXX XX XX XX D1S548 172/172 172/172 172/172 172/172 172/172 172/172D2S1333 293/301 297/305 293/301 293/301 293/301 293/301 D3S1768 192/196184/192 192/196 192/196 192/196 192/196 D4S2365 284/296 296/296 284/296284/296 284/296 284/296 D4S413 123/123 133/153 123/123 123/123 123/123123/123 D5S1457 115/123 123/123 115/123 115/123 115/123 115/123 D6S501172/172 164/172 172/172 172/172 172/172 172/172 D7S513 179/189 179/193179/189 179/189 179/189 179/189 D9S921 183/183 183/203 183/183 183/183183/183 183/183 D10S1412 162/171 162/165 162/171 162/171 162/171 162/171D11S2002 254/254 254/254 254/254 254/254 254/254 254/254 D11S925 282/295297/303 282/295 282/295 282/295 282/295 D12S364 264/276 266/272 264/276264/276 264/276 264/276 D12S67 252/260 252/264 252/260 252/260 252/260252/260 D13S765 188/192 192/200 188/192 188/192 188/192 188/192 D16S403141/141 137/139 141/141 141/141 141/141 141/141 D17S1300 257/257 257/269257/257 257/257 257/257 257/257 D18S537 196/200 196/204 196/200 196/200196/200 196/200 D18S72 305/305 305/305 305/305 305/305 305/305 305/305DXS2506 282/282 278/278 282/282 282/282 282/282 282/282 MFGT22 104/108104/108 104/108 104/108 104/108 104/108 D6S291 201/209 245/249 201/209201/209 201/209 201/209 G51152 213/213 ND 213/213 213/213 213/213213/213 MICA 183/195 ND 183/195 183/195 183/195 183/195 MOGCA 121/137 ND121/137 121/137 121/137 121/137 D6S276 251/251 199/209 251/251 251/251251/251 251/251 D6S1691 223/237 213/213 223/237 223/237 223/237 223/237

TABLE 5 Somatic mtDNA carryover in human NT-ESCs mtDNA heteroplasmy %Cell line (±sd) hESO-NT1 4.6 ± 0.7 hESO-NT2 2.8 ± 0.3 hESO-NT3 1.2 ± 0.2hESO-NT4 4.9 ± 0.7 Average 3.4 ± 1.7

Lastly, a comparative microarray expression analysis of the hESO-NT1cell line was performed relative to the IVF control hESO-7 and parentalsomatic HDF-f using the Affymetrix PrimeView platform. Initially, threebiological replicates within each sample were compared against eachother. For comparisons, the detected signal for each probe set wasplotted in a scatter graph and the correlation value was calculated.This assay demonstrated 99% transcriptional correlation within each celltype suggesting that minimal variations existed between biologicalreplicates collected from different culture plates (FIG. 14).

Next, each NT-ESC and IVF-ESC types were compared against each other andto somatic cells (HDF-f). As expected, both stem cell types displayedlow transcriptional correlation to fibroblasts (FIG. 7A and FIG. 7B).Among 50 genes with the highest fold change, many known pluripotencygenes were observed including LIN28, POU5F1, NANOG, and SOX2 (Table 6).In contrast, ESCs derived by IVF and SCNT were similar to each other(FIGS. 7A and B). Some transcriptional differences between human NT-ESCsand IVF-ESCs were observed, however no known pluripotency genes wereincluded in this list (Table S7 and S8). Interestingly, an HLA-C majorhistocompatibility gene was highly downregulated in hESO-NT1 comparedwith hESO-7 (79 fold) (Table 8).

TABLE 6 Genes highly expressed in human NT-ESCs (hESO-NT1 and controlIVF-ESCs (hESO-7) compared to parental fibroblasts. Gene expression foldAffymetrix Gene change* No. Probe Set ID Gene Name symbol hESO-7hESO-NT1 1 11725430_at Lin-28 homolog LIN28 758 750 2 11723364_at LINE-1type transposase L1TD1 435 381 domain containing 1 3 11720993_at SRY(sex determining region Y)- SOX2 429 395 box 2 4 11723191_at Zic familymember 2 ZIC2 418 373 5 11717386_s_at Metallothionein 1G MT1G 343 168 611755599_x_at POU class 5 homeobox 1 POU5F1 340 316 7 11736127_s_atDevelopmental pluripotency DPPA4 340 295 associated 4 8 11730462_s_atOrthodenticle homeobox 2 OTX2 326 381 9 11719444_s_at Protein tyrosinephosphatase, PTPRZ1 316 321 receptor-type, Z polypeptide 1 1011740301_a_at Ubiquitin specific peptidase 44 USP44 314 261 1111745651_a_at Epithelial cell adhesion molecule EPCAM 312 347 1211716906_a_at Cadherin 1, type 1, E-cadherin CDH1 286 200 (epithelial)13 11759218_at Zic family member 3 ZIC3 283 220 14 11733551_at Zicfamily member 5 ZIC5 252 238 15 11720460_x_at F11 receptor F11R 247 22316 11746506_a_at Secreted phosphoprotein 1 SPP1 241 340 17 11719869_a_atV-myc myelocytomatosis viral MYCN 241 221 related oncogene, 1811727909_at Solute carrier family 7 (cationic SLC7A3 240 226 amino acidtransporter, y+ system), member 3 19 11747223_a_at Endothelin receptortype B EDNRB 230 245 20 11723543_a_at Epithelial splicing regulatoryESRP1 222 191 protein 1 21 11746022_s_at teratocarcinoma-derived growthTDGF1 210 227 factor 1 22 11758000_s_at Coxsackie virus and adenovirusCXADR 205 204 receptor 23 11725749_a_at Galanin prepropeptide GAL 203308 24 11725436_a_at Secretoglobin, family 3A, member 2 SCGB3A2 200 18225 11729643_s_at Tumor protein D52 TPD52 194 165 26 11734366_x_at Zincfinger protein 42 homolog ZFP42 190 186 27 11733474_at SRY (sexdetermining region Y)- SOX21 185 122 box 21 28 11721990_at Leukocytecell derived LECT1 183 135 chemotaxin 1 29 11716017_at Mal, T-celldifferentiation protein 2 MAL2 181 179 30 11719684_a_at Neurotensin NTS157 255 31 11725237_a_at RNA binding protein with RBPMS2 157 163multiple splicing 2 32 11734427_at Tripartite motif-containing 71 TRIM71154 138 33 11757573_s_at Frizzled homolog 5 FZD5 148 115 3411755164_a_at Left-right determination factor 1 LEFTY1 147 117 3511731121_s_at Vasohibin 2 VASH2 147 90 36 11727987_a_at DNA(cytosine-5-)- DNMT3B 137 110 methyltransferase 3 beta 37 11748773_a_atCathepsin L2 CTSL2 134 169 38 11718350_s_at NLR family, pyrin domainNLRP2 132 88 containing 2 39 11757625_s_at CD200 molecule CD200 128 13340 11729429_a_at Kinesin family member 26A KIF26A 127 105 4111757702_s_at Desmocollin 2 DSC2 118 146 42 11732577_x_at Nanog homeoboxNANOG 111 154 43 11728591_at Hypothetical protein LOC729993 LOC729993111 127 44 11759881_at Peptidylprolyl isomerase A PPIA 103 114(cyclophilin A) 45 11756165_s_at Glycine dehydrogenase GLDC 102 116(decarboxylating) 46 11747042_a_at Contactin associated protein-like 2CNTNAP2 91 142 47 11725524_s_at Desmoglein 2 DSG2 91 91 48 11731989_atHESX homeobox 1 HESX1 91 73 49 11758166_s_at Kallmann syndrome 1sequence KAL1 88 124 50 11732657_a_at Cytochrome P450, family 26,CYP26A1 88 110 subfamily A, polypeptide 1

TABLE 7 Highly upregulated genes in NT-ESCs (hESO-NT1) compared toIVF-ESC (hESO-7) Affymetrix Gene expression fold No. Probe Set ID GeneName Gene symbol change* 1 11755911_a_at G protein-coupled receptor 128GPR128 115 2 11722472_a_at paternally expressed 3 MEG3 26 3 11728941_atChromosome 13 open reading C13orf38 12 frame 38 4 11740844_s_at VonWillebrand factor D and EGF VWDE 11 domains 5 11737126_x_at Similar toCTAGE6 LOC441294 8 6 11720703_at Myosin, light chain 4, alkali; atrial,MYL4 5 embryonic 7 11736163_a_at Cyclin-dependent kinase inhibitorCDKN2B 4 2B (p15, inhibits CDK4) 8 11759120_a_at Leucine-richrepeat-containing G LGR5 4 protein-coupled receptor 5 9 11746373_s_atRRN3 RNA polymerase 1 RRN3 4 transcription factor homolog 10 11727675_atMolybdenum cofactor sulfurase MOCOS 4 11 11760343_x_at zinc fingerprotein 726 ZNF726 4 12 11717912_s_at Chemokine (C—X—C motif) ligandCXCL14 4 14 13 11735201_x_at NEDD4 binding protein 2 N4BP2 4 1411744894_at Family with sequence similarity 20, FAM20A 4 member A 1511764141_x_at Solute carrier family 25 SLC25A1 4 (mitochondrial carrier,citrate transporter), member 1 16 11757096_s_at Zinc finger protein 98(F7175) ZNF98 4 17 11718766_at Protease, serine, 23 PRSS23 3 1811729820_at Up-regulated during skeletal USMG5 3 muscle growth 5 homolog19 11756542_a_at G protein-coupled receptor 87 GPR87 3 20 11719120_a_atKynureninase (L-kynurenine KYNU 3 hydrolase) 21 11750167_a_at Calpain 2,(m/II) large subunit CAPN2 3 22 11727117_at Natriuretic peptideprecursor B NPPB 3 23 11744435_a_at Dual specificity phosphatase 6 DUSP63 24 11716433_s_at Stearoyl-CoA desaturase 5 SCD5 3 25 11715796_s_atLumican LUM 3

TABLE 8 Highly downregulated genes in human NT-ESCs Affymetrix Geneexpression fold No. Probe Set ID Gene Name Gene symbol change* 111715316_x_at Major histocompatibility complex, HLA-C 79 class 1, C 211763252_x_at Phosphoserine phosphatase PSPH 9 3 11730995_a_at Actinin,alpha 3 ACTN3 6 4 11759838_x_at Zinc finger protein 506 ZNF506 5 511747933_a_at Nicotinate phosphoribosyltransferase NAPRT1 5 domaincontaining 1 6 11720803_at S100 calcium binding protein A14 S100A14 4 711716034_a_at Bone marrow stromal cell antigen 2 BST2 4 8 11720549_a_atPeroxisomal biogenesis factor 6 PEX6 4 9 11746500_x_at glutathioneS-transferase omega 2 GSTO1 3 10 11755044_x_at Pigeon homolog PION 3 1111726063_a_at Chromosome 2 open reading frame C2orf40 3 40 1211732934_a_at Developmental pluripotency DPPA5 3 associated 5 1311730250_a_at Ligand of numb-protein X 1 LNX1 3 14 11733305_a_atTranscription factor AP-2 beta TFAP2B 3 (activating enhancer bindingprotein 2 beta) 15 11728437_at Bromodomain and WD repeat BRWD1 3 domaincontaining 1 16 11734175_a_at Chromosome 13 open reading frame C13orf383 38 17 11728244_s_at Solute carrier family 12 SLC12A1 3(sodium/potassium/chloride transporters), member 1 18 11755819_a_at DEAD(Asp-Glu-Ala-Asp) box DDX58 2 polypeptide 58 19 11746803_s_atDevelopmental pluripotency DPPA3 2 associated 3 20 11717191_a_atTroponin C type 2 (fast) TNNC2 2 21 11731771_at Protocadherin beta 15PCDHB15 2 22 11719028_a_at Pleckstrin and Sec7 domain PSD3 2 containing3 23 11718230_a_at Major histocompatibility complex, HLA-F 2 class I, F24 11743972_a_at DNA-damage-inducible transcript 4 DDIT4 2 2511725196_a_at Zinc finger, SWIM-type containing 7 ZSWIM7 2

Example 7—Procedures

Rhesus Macaque SCNT:

Oocyte collections, SCNT, embryo culture and NT-ESC isolation procedureswere performed as previously described (Byrne et al, 2007 supra; Sparmanet al., 2009, supra; Sparman et al, 2010 supra).

Human Oocyte Donations:

Anonymous oocyte donors of age 23-31 were recruited through the OHSUWomen's Health Research Unit via print and web-based advertising.Responding women were screened with respect to their reproductive,medical and psychosocial health. Healthy and non-obese (BMI<28 kg/m²)women, who passed the initial medical and psychological evaluations,were invited to a research egg donation.

Ovarian stimulation protocols followed established clinical IVFguidelines as we described previously (Tachibana et al, 2013 supra).Briefly, a combination of recombinant follicle stimulating hormone(rFSH) and human menopausal gonadotropins (hMG) and either GnRH agonist(Lupron®, Tap Pharmaceutical Products, Lake Forest, Ill.) or antagonist(Ganirelix®, Merck & Co, Whitehouse Station, N.J.) were given. Humanchorionic gonadotropin (hCG) was prescribed to trigger oocytematuration. Self administration of injectable rFSH (sc, Follistim®,Merck & Co, Whitehouse Station, N.J.) commenced on cycle day 2 or 3 andcontinued for approximately 8-12 days. The starting gonadotropin dosewas 75-125 IU/day and 1-2 A hMG (sc, Menopur®, Ferring Pharmaceuticals,Inc. Parsippany, N.J.); the dose was adjusted per individual responseusing an established step-down regimen until the day of hCG injection.Ovarian response and follicular growth were monitored by transvaginalultrasound and measurements of serum estradiol levels. When two or morefollicles reached >18 mm in diameter, subjects received hCG (1041U, sc,Ovidrel®, EMDSerono, Rockland, Mass.) to trigger maturation. Thirty-sixhours following hCG injection, subjects underwent oocyte retrieval viatransvaginal follicular aspirations.

Cumulus-oocyte complexes (COCs) were collected from aspirates and placedin HTF w/HEPES medium (LifeGlobal®, IVFonline, LLC) supplemented with10% Serum Protein Substitute (Quinns Advantage Serum®, CooperSurgical,INC) (HTF w/HEPES 10%) at 37° C. COCs were treated with hyaluronidase todisaggregate cumulus and granulosa cells. Oocytes were isolated andclassified as germinal vesicle, meiotic metaphase I (MI) and maturemetaphase II (MII) stage, and then placed in Global® medium(LifeGlobal®, IVFonline, LLC) supplemented with 10% Serum ProteinSubstitute (Quinns Advantage Serum®, CooperSurgical, INC) (Global 10%)at 37° C. in 5% CO₂ and covered with tissue culture oil (Sage IVF®,Cooper Surgical, Inc).

Nuclear Donor Cell Preparations:

Commercially available female dermal fibroblasts of fetal origin (HDF-f)were obtained from ScienCell Research Laboratories. Cells were expandedin 75 cm³ cell culture flasks (Corning) containing DMEM/F12 supplementedwith 100 IU ml-1 penicillin, 100 μg ml-1 streptomycin (Invitrogen), 10%FBS at 37° C. in 5% CO₂. Fibroblasts were then disaggregated withtrypsin treatment and frozen down in aliquots of 3×10⁵ cells in mediumcontaining 10% dimethyl sulphoxide (DMSO). Cells were subsequentlythawed prior to the SCNT and cultured in 4-well dishes (Nunc) understandard conditions until confluency. Confluent cells were synchronizedin the G₀/G₁ phase of the cell cycle by culture in DMEM/F12 medium with0.5% FBS for 2-4 days before SCNT.

Human SCNT Procedures and Embryo Culture:

Enucleation of MII spindles were performed as described previously(Tachibana et al., 2013 supra). Oocytes were placed into 50 μlmanipulation droplet of HTF w/HEPES 10% medium containing 5 μg/mlcytochalasin B and 1.25 mM caffeine in a glass-bottom dish. The dropletwas covered with tissue culture oil and oocytes maintained at 37° C. for10-15 min before spindle removal. The dish was then mounted on the stageof an inverted microscope (Olympus IX71®) equipped with a stage warmer(http://www.tokaihit.com) Narishige micromanipulators, Oosight™ ImagingSystem (www.cri-inc.com) and a laser objective (www.hamiltonthorne.com).An oocyte was positioned by a holding pipette so that the spindle wassituated between the 2 o'clock and 4 o'clock position. The zonapellucida next to the spindle was drilled with a laser pulse and anenucleation pipette was inserted through the opening. A small amount ofcytoplasm surrounded by plasma membrane and contacting spindle wasaspirated into the pipette. Next, a disaggregated fibroblast wasaspirated into a micropipette and briefly transferred to the dropcontaining HVJ-E extract (Ishihara Sangyo Kaisha Ltd). The cell was thenplaced into the perivitelline space of the cytoplast on the sideopposite the first polar body. SCNT constructs were rinsed with HTFw/HEPES 10%, transferred to Global 10% medium and incubated at 37° C. in5% CO₂ for 30 min until fusion. Successful fusion was confirmed visually30 min by the disappearance of the donor cell in the perivitellinespace. Reconstructed oocytes were then subjected to artificialactivation consisting of electroporation pulse (two 50 μs DC pulses of2.7 kV cm⁻¹) (Electro Square Porator T-820, BTX, Inc.) in 0.25 Md-sorbitol buffer containing 0.1 mM calcium acetate, 0.5 mM magnesiumacetate, 0.5 mM HEPES and 1 mg ml-1 fatty-acid-free BSA. Activated SCNTconstructs were then incubated in Global® medium (w/o serum) containing2 mM DMAP at 37° C. in 6% CO2 for 4 h. After DMAP, SCNT embryos wererinsed with HTF w/HEPES 10% SSS and transferred into 4-well dishescontaining Global® medium supplemented with 10% FBS, 12 μMβ-mercaptoethanol (BME), 10 nM Trichostatin A (TSA, Sigma) and culturedat 37° C. in 6% CO₂, 5% O₂ and 89% N₂ for 12 hours. Embryos were thenrinsed, checked for pronuclear formation and cultured in Global® mediumsupplemented with 10% FBS and 12 μM β-mercaptoethanol (BME) at 37° C. in6% CO₂, 5% O₂ and 89% N₂ for a maximum of 7 days. Medium was changedonce at day 3 of culture.

Isolation, Culture and Characterization of Human NT-ESCs:

After removal of the zona pellucida with a brief exposure to 0.5%protease (Sigma), SCNT blastocysts were plated onto confluent feederlayers of mitomycin C inactivated mouse embryonic fibroblasts (mEFs) andcultured for 5-7 days at 37° C., 3% CO₂, 5% O₂ and 92% N₂ in ESCderivation medium. The derivation medium consisted of DMEM/F12(Invitrogen) supplemented with 0.1 mM nonessential amino acids, 1 mM1-glutamine, 0.1 mM β-mercaptoethanol, 5 ng/ml basic fibroblast growthfactor, 10 μM ROCK inhibitor (Sigma), 10% FBS and 10% knockout serumreplacement (KSR; Invitrogen). Before use, fresh ESC derivation mediumwas mixed (50%:50%, v/v) with derivation medium conditioned for 24 hculture with growing human ESCs. Outgrowths of the inner cell mass (ICM)were manually dissociated into small clumps with a microscalpel andreplated on fresh mEF plates. After the first passage of ICM outgrowth,FBS and ROCK inhibitor were omitted and KSR was increased to 20%.Colonies with ESC-like morphologies were selected for furtherpropagation, characterization and cytogenetic analyses.Immunocytochemistry, in vivo and in vitro differentiation and microarrayanalyses were performed as described (Byrne et al, 2007 supra; Mitalipovet al, 2007 supra; Tachibana et al, 2013 supra). Detailed protocols arealso available in Supplemental procedures.

Nuclear DNA Genotyping and Cytogenetic Analyses:

Genotyping of NT-ESCs was performed by microsatellite typing using 23markers representing 22 human autosomal loci and one X-linked locus aspreviously described (Tachibana et al, 2013 supra). Karyotyping wasperformed by GWT-banding on 20 metaphase cells from each human NT-ESCline at the Human Genetics Laboratory, University of Nebraska MedicalCenter as previously described (Tachibana et al, 2013 supra).

MtDNA Genotyping:

Genotyping of mtDNA was performed as previously described (Tachibana etal, 2013 supra). The region of human mitochondrial displacement loop(D-loop) harboring the hypervariable segment 1(HSV-1) was amplifiedusing published primers (Danan C et al, Am J Hum Genetics 65, 463-473(1999)). PCR products were sequenced and the informative singlenucleotide polymorphic (SNP) sites were identified using Sequencher® v.4.7 software (GeneCodes). Quantitative mtDNA analysis was performed byARMS-qPCR as described (Tachibana et al, 2013 supra).

Immunocytochemistry:

Immunocytochemical analysis was performed as previously described(Tachibana et al, 2013 supra) using antibodies for OCT-4, SOX2, TRA1-60,TRA1-81, and SSEA-4 from Applied StemCell. NANOG antibody was from R&DSystems, Inc. Nuclei were labeled with DAPI (Molecular Probes).

Teratoma Assay:

Approximately 3-5 million of undifferentiated ESCs were injected intothe hind-leg muscle of 4-week-old, SCID, beige male mice using an 18gauge needle. Six to seven weeks after injection, mice were euthanizedand tumors dissected, sectioned and histologically characterized for thepresence of representative tissues as described previously (Tachibana etal, 2013 supra).

Cardiac Differentiation:

Differentiation into cardiac cells was initiated by embryoid bodyformation in a suspension culture as described (Byrne et al, 2007supra). Briefly, ESC colonies were loosely detached from feeder cellsand transferred into feeder-free, 6-well, ultra-low adhesion plates(Corning Costar) and cultured in suspension in ESC medium supplementedwith 20% FBS but without FGF for 5-7 days. Embryoid bodies were thenplated into collagen-coated dishes and cultures were maintained in ESCmedium for additional 2-4 weeks until spontaneously contractingcardiomyocytes were observed.

ARMS-qPCR Assay:

The Amplification Refractory Mutation System quantitative PCR assay wasperformed to measure mtDNA carryover levels in ESCs as previouslydescribed (Tachibana et al., 2013). Primers and TaqMan® MGB probes weredesigned to detect unique mtDNA SNPs between HDF-f skin fibroblast donorcells and egg donor mtDNA haplotypes. The non-discriminative anddiscriminative assays were mixed and measured with Rotor-Gene® MultiplexPCR Kit (Qiagen). PCR reactions (15 μl) containing 1×PCR Master Mix,100-250 nM each primer, 150 nM each TaqMan probe and about 1-4 ng oftotal genomic DNA were performed according to the manufacturer'sinstructions. The fluorescent signal intensities were recorded andanalyzed during PCR in an ABI 7900HT® fast real-time PCR system (AppliedBiosystems) using SDS® (Ver. 2.4) software. All reactions were run induplicate with two different amounts of input DNA: 1-4 ng and 1:8dilutions. The SDS software generated a standard curve using four 8-folddilutions plus a last 4-fold dilution. The percentage of carryover mtDNAin relation to the total mtDNA content was calculated by the equationheteroplasmy=100*(Quantity D/Quantity ND).

Transcriptional Profiling by Microarray:

Comparative microarray analysis of mRNA for hESO-NT1, hESO-7 and HDF-fwas carried out using the Affymetrix PrimeView® human genome array. RNAsamples were converted to labeled cRNA and hybridized to PrimeView HumanGene Expression Array (Affymetrix, Inc.). The distribution offluorescent material on the processed array was determined using theGeneChip Scanner 3000° with the 7G upgrade (Affymetrix) and AGCC version3.2 software (Affymetrix), yielding cell fluorescence intensity (.celfiles). Image inspection was performed manually immediately followingeach scan. Processed image files were normalized across arrays using therobust multichip average algorithm (Irizarry R A et al, Biostatistics 4249-264 (2003)) and log transformed (base 2) to perform directcomparisons of probe set values between samples. GeneSifter® (VizX Labs,Seattle, Wash.) microarray expression analysis software was used toidentify differentially expressed transcripts. For a given comparison,IVF-derived ESCs were selected as the baseline reference, andtranscripts that exhibited various fold change relative to the baselinewere considered differentially expressed. To facilitate in-depthcomparisons, processed image files were normalized with the robustmultichip average algorithm and log transformed (base 2) using theStatView® program. Corresponding microarray expression data wereanalyzed by pairwise differences determined with the Student-t-test(P<0.05).

Statistics:

For embryo development and clinical parameters, statistical analyseswere performed using ANOVA or t-test with Statview® Software (SASInstitute, Inc.) with statistical significance set at 0.05. ESCisolation efficiencies were analyzed using chi square with statisticalsignificance set at 0.05.

Example 8—Comparison of Pluripotent Stem Cells Derived from Somatic CellNuclear Transfer with Those Derived by IVF and Induced Pluripotent StemCells

Human pluripotent stem cells hold great potential for regenerativemedicine, but available cell types have important limitations. Whileembryonic stem cells derived from fertilized embryos (IVF-ESCs) areconsidered the “gold standard” of pluripotency, they are allogeneic topotential recipients. Likewise, autologous induced pluripotent stemcells (iPSCs) are prone to epigenetic and transcriptional aberrations.To determine whether accumulation of such aberrations is intrinsic tosomatic cell reprogramming or secondary to the reprogramming method, agenetically matched collection of human IVF-ESCs, iPSCs, and ESCsderived by somatic cell nuclear transfer (SCNT; NT-ESCs) were generatedand subjected to genome-wide genetic, epigenetic and transcriptionalanalyses. SCNT-based reprogramming is mediated by the full complement ofoocyte cytoplasmic factors, thus closely recapitulating earlyembryogenesis. NT-ESCs and iPSCs derived from the same somatic donorcells contained comparable numbers of de novo copy number variations(CNVs), suggesting that the two reprogramming methods may not differsignificantly in terms of mutagenic or selective pressure.

In contrast, the DNA methylation and transcriptome profiles of NT-ESCscorresponded very closely to those of IVF-ESCs, while iPSCs differedmarkedly from IVF-ESCs and harbored residual DNA methylation patternstypical of parental fibroblasts, suggesting incomplete reprogramming. Weconclude that human somatic cells can be faithfully reprogrammed topluripotency by SCNT and are, therefore, ideal candidates for cellreplacement therapies.

Background:

The derivation of human ESCs from in vitro fertilized embryos (Thomson JA et al, Science 282, 1145-1147 (1998)) was met with enthusiasm due totheir potential use in cell-based therapies, tempered only by therecognition that lifelong immunosuppression would be required forengraftment and survival of allogeneic IVF-ESCs. The advent of iPSCtechnology (Takahashi K et al, Cell 131, 861-872 (2007) and Rais Y etal, Nature 502, 65-70 (2013)) overcomes this limitation, sincepatient-matched cells can be produced relatively easily andeconomically.

However, concerns have recently arisen due to the high frequency ofgenetic and epigenetic abnormalities observed in iPSCs, includingsubchromosomal duplications and deletions detected as copy numbervariations (CNVs) (Hussein S M et al, Nature 471, 58-62 (2011) andLaurent L C et al, Nature Comm 4, 1382 (2013)), protein-coding mutations(Ruiz S et al, Nature Comm 4, 1382 (2013)) and defects in DNAmethylation and gene expression at regions subject to imprinting and Xchromosome inactivation (Nazor K L et al, Cell Stem Cell 10 620-634(2012); Lister R et al, Nature 471, 68-73 (2011); Ohi Y et al, NatureCell Biol 13, 541-549 (2011); and Ruiz S et al, Proc Nat/Acad Sci USA109, 16196-16201 (2012)).

While it is not yet understood whether these aberrant epigenetic marksreflect errors arising during reprogramming or incomplete reversion topluripotency, these abnormalities could impact the accuracy of in vitrodisease modeling or the utility of iPSCs for regenerative medicine. Withthe availability of SCNT as an alternative approach to somatic cellreprogramming (Tachibana M et al, Cell 153, 1228-1238 (2013)), a studyto explore the mechanisms underlying transcription factor- andSCNT-based reprogramming was initiated.

Although the molecules responsible for SCNT-based reprogramming remainlargely unknown, it is generally accepted that the cytoplasmic factorsinvolved are different from those used for generation of iPSCs. Forinstance, OCT4 plays a critical role in the induction and maintenance ofpluripotency in iPSCs but is not required in oocyte-based reprogramming(Wu G et al, Nature Cell Biol 15, 1089-1097 (2013)).

The hypothesis that distinct mechanisms underlying SCNT- andfactor-based reprogramming lead to differences in the genetic andepigenetic stability of the resulting pluripotent cells was tested. Amatched collection of NT-ESC and iPSC lines was generated from the sameparental somatic cells. As controls, IVF-ESCs were produced usingoocytes from the same donor who provided the providing oocytes for SCNT.We subjected the cell lines to high-resolution genetic, epigenetic andtranscriptional analyses, thereby defining the distinct molecularprofiles of each pluripotent stem cell type.

Derivation of Genetically Matched Lines:

Four human NT-ESC lines from fetal dermal fibroblasts (HDFs), designatedNT1-4 were previously generated (See Tachibana et al, 2013 supra).Described herein, generated genetically matched iPSCs from the same HDFculture were also generated. Two reprogramming vectors were used; 1)integrative retroviral vectors carrying OCT4, SOX2, KLF4, and MYC (LowryW E et al, Proc Nat/Acad Sci USA 105, 2883-2888 (2008)) and 2)non-integrative Sendai virus-based vectors carrying the same fourfactors (Fusaki N et al, Proc Japan Acad Series B 85, 348-362 (2009)).Colonies were randomly based on typical ESC-morphology. Five iPSCclones/lines produced from the Sendai technique were expanded anddesignated iPS-S1-5. Two lines produced from retroviral transductionwere expanded and designated iPS-R1 and -R2.

Two IVF-ESC lines, designated hESO-7 and -8, were derived fromblastocysts generated by IVF of oocytes from the same donor that wereused for SCNT. All cell lines were generated in one laboratory and thepassaging and culture conditions were identical. Similar to IVF-ESCs andNT-ESCs, all iPSC lines maintained typical ESC morphology, expressedpluripotency markers (Tachibana et al, 2011 supra, and Tachibana M etal, Nature 493, 627-631 (2013)) and were capable of forming teratomascontaining cells representing all three germ lineages. CytogeneticG-banding analysis confirmed that all pluripotent cell lines retained adiploid karyotype with no detectable numerical or structural chromosomalabnormalities.

Short tandem repeat (STR)-based genotyping using 1 marker for genderdetermination (AME) and 22 distinct markers distributed over 16chromosomes (15 autosomes and the X chromosome) verified that all NT-ESCand iPSC lines were genetically matched to each other and to theoriginal HDFs. The only line that did not show perfect concordance forall 23 STR markers was the iPS-R1cell line which displayed homozygosityat the D3S1768 locus on chromosome 3 compared to the HDFs and otherreprogrammed cell lines, which were all heterozygous at this locus. Thissuggested that a loss-of-heterozygosity had occurred in the iPS-R1cellline.

High-resolution microarray-based single nucleotide polymorphism (SNP)genotyping was performed to allow detailed genetic comparisons amongstem cells, parental HDFs and oocyte and sperm donors. Replicate ErrorAnalysis confirmed that all NT-ESC and iPSC lines, excluding iPS-R1,were essentially identical to each other and to the parental HDFs(>99.96% similarity). Notably, iPS-R1 displayed a higher number ofdifferences compared to HDFs (99.855% similarity). Consistent with theSTR analysis, this line displayed a large de novo region of homozygosity(ROH) on chromosome 3. SNP genotyping indicated that the oocyte andsperm donors were unrelated to HDFs, NT-ESCs and iPSCs (88.859-88.987%similarity). Finally, we verified the first-degree genetic relationshipsbetween two IVF-ESC lines and both the oocyte and sperm donors(92.554-94.23% similarity).

Based on the sequencing data within the D-loop hypervariable region ofthe mitochondrial genome (mtDNA), the mtDNA in NT-ESCs was largelyoocyte-derived. Here, using whole genome bisulfite sequencing(MethylC-Seq) and transcriptome sequencing (RNA-Seq), it was shown that,as expected, the entire mitochondrial genome in all four NT-ESC linesand two IVF-ESCs was nearly identical, which was an expected outcome, asall the oocytes were provided by the same donor. However, the mtDNAsequences of these lines differed at 13 nucleotide positions whencompared to HDFs or iPSCs, a result that was confirmed by conventionalSanger sequencing. The NT4 cell line showed C/T heteroplasmy at mtDNAposition 16092, while the other NT-ESC and IVF-ESC lines contained ahomoplasmic C allele. RNA-Seq analysis also detected a small amount ofmtDNA carryover from the HDF in 3 out of 4 NT-ESC lines, ranging from 1%to 4.9%. Quantification was based on the relative number of oocyte- andHDF-specific reads at informative SNPs and the results were consistentwith heteroplasmy measurements in NT-ESCs performed by ARMS-qPCR.

Subchromosomal Genetic Aberrations:

To detect de novo genetic aberrations arising during reprogramming, wecompared high-throughput SNP genotyping from early passage iPSCs andNT-ESCs (passage 5-6) to HDFs, thereby allowing the recognition andremoval of pre-existing aberrations. A total of thirteen de novo CNVsranging in size from 6 to 52,696 kb were identified including ten iniPSCs and three in NT-ESCs. NT3 carried a one-copy deletion onchromosome 16 and NT4 had two duplications, one each on chromosome 3 and6. No CNV abnormalities were detected in NT1 and NT2. Multiple CNVs wereidentified in four iPSC lines; iPS-S1 harbored two duplications onchromosomes 1 and 5, iPS-S2 had three one-copy deletions on chromosomes1, 4 and 17, and iPS-S3 carried a single one-copy deletion on chromosome10. Line iPS-R1 displayed two duplications on chromosomes 3 and 4, onelarge ROH encompassing most of the short arm of chromosome 3 and onetwo-copy deletion within the ROH. As indicated above,loss-of-heterozygosity in this region of chromosome 3 was also confirmedby independent STR analysis. No CNV abnormalities were detected iniPS-S4, iPS-S5 and iPS-R2. All CNVs detected by SNP genotyping analysiswere validated using normalized RNA-Seq read counts qPCR or STRanalysis. In comparing IVF-ESCs to oocyte and sperm donor DNA (Ben-YosefD et al, Cell Reports 4, 1288-1302 (2013)), a single one-copy deletionon the X chromosome was identified in hESO-7.

To further evaluate genetic stability, SNP genotyping was performed on asecond group of matched samples, consisting of two NT-ESC lines(Leigh-NT1 and Leigh-NT2) derived from a patient with Leigh syndrome,and three matched Sendai iPSC lines (Leigh-iPS1, Leigh-iPS2, andLeigh-iPS3). Cytogenetic G-banding analysis demonstrated that all butone of the Leigh cell lines retained a diploid male karyotype with nodetectable numerical or chromosomal abnormalities. Leigh-NT2 had atetraploid karyotype, and was therefore excluded from further analysis.STR genotyping corroborated that Leigh-NT1 and the three Leigh-iPSClines were genetically matched to the parental fibroblasts. It was alsoconfirmed that Leigh-NT1 carried oocyte mtDNA while all Leigh-iPSCsinherited the Leigh-fib mitochondrial genome including the homoplasmicm.8993T→G mutation (Taylor R W and Turnbull D M, Nature Rev Genet 6,389-402 (2005)). A total of nine de novo CNVs were identified in Leighcell lines, including multiple CNVs in Leigh-iPS1 and -iPS3 and one eachin Leigh-iPS2 and Leigh-NT1.

Based on the total number of CNVs detected, it was calculated that iPSCs(ten cell lines), NT-ESCs (5 cell lines) and IVF-ESCs (2 cell lines)carried an average of 1.8, 0.8 and 0.5 CNVs per cell line, respectively.No significant differences were found among pluripotent stem cell types.The InDel analysis of RNA-Seq data from the same set of humanpluripotent stem cell lines also indicated that NT-ESC lines had fewerInDels compared to the iPSC lines, but the difference was notsignificant. However, these results are consistent with a previousreport that iPSCs, on average, carry 2 de novo CNVs per line (Abyzov A,Nature 492, 438-442 (2012)). None of the identified CNVs were sharedamong cell lines. In addition, there was not a higher average incidenceof genomic aberrations in the retrovirus-derived iPSC lines relative tothe non-integrating Sendai virus-induced iPSCs.

Since the NT-ESCs and the iPSCs were generated from the same somaticcells and did not contain statistically significant different numbers ofCNVs, it appears that the mutagenic and selective pressures present intranscription factor-based and SCNT-based reprogramming are similar inmagnitude.

Global DNA Methylation:

DNA methylation is an important epigenetic mechanism contributing tocell identity. Significant DNA methylation differences between iPSCs andIVF-ESCs have been reported, as well as differences among iPSC lines(Nazor K L 2012 supra and Bock C et al, Cell 144, 439-452 (2011)). Sincesuch differences could reflect incomplete or abnormal reprogramming andresult in altered gene expression affecting cell function, the matchedstem cell lines derived from the HDF somatic cells using the wereprofiled using an Infinium HumanMethylation450 BeadChip® to characterizethese differences on a genome-wide scale (Price M E et al, PLoS Genetics7, e1002389 (2011)). To determine whether global DNA methylationpatterns were similar to previously reported cell lines (Ziller M J etal, PLoS Genetics 7, e1002389 (2011)); unsupervised hierarchicalclustering was performed (Suzuki R and Shimodaira H et al,Bioinformatics 22, 1540-1542 (2006)).

Bootstrap resampling analysis revealed two well-defined clusters, onecontaining seven iPSC lines (including the four iPSC lines generatedherein; FIG. 15A) and one IVF-ESC line (HUES64). The second clusterincluded four NT-ESC lines and four IVF-ESC lines (FIG. 15A). Based onthis comparison, we determined that NT-ESCs clustered together withIVF-ESCs (with the exception of HUES64) while iPSCs formed a distinctgroup. To ensure that intra-group variability was similar between theiPSCs, NT-ESCs and IVF-ESCs the coefficient of variation (CV) wascalculated for each stem cell type and compared to previously reportedcell lines (iPSC=0.71, NT-ESC=0.73, IVF-ESC=0.74; Ziller et al.iPSC=0.73 and IVF-ESC=0.72,).

Comprehensive group-wise analysis revealed 6,478 differentiallymethylated probes (DMPs) between iPSCs and IVF-ESCs (FDR<0.01; FIG.15B). Using the same criteria, only 110 DMPs were found between theNT-ESCs and IVF-ESCs, suggesting that in contrast to iPSCs, NT-ESCs wereremarkably similar to IVF-ESCs. It was then determined whether or notthe DMPs identified in iPSCs and NT-ESCs could be attributed to residualepigenetic memory inherited from HDFs. Of the 6,478 DMPs identified iniPSCs, 780 displayed a substantial difference in DNA methylation (Avg. βdifference>10.31) both between iPSCs and IVF-ESCs and between HDFs andIVF-ESCs. Of the 110 DMPs identified in NT-ESCs, 87 were substantiallydifferent both between NT-ESCs and IVF-ESCs and between HDFs andIVF-ESCs (FIG. 15B). Functional enrichment analysis of probes that werehighly methylated in iPSCs and HDFs compared to IVF-ESCs indicatedassociation with sequence-specific DNA binding transcription factoractivity (2.02 Fold Enrichment, FDR<0.0001). No significant annotationterms were found for hypermethylated probes shared by NT-ESCs and HDFs.However, probes that were hypomethylated in iPSCs, NT-ESCs and HDFscompared to IVF-ESCs were enriched for loci associated with the MHCclass II protein complex (72 Fold Enrichment, FDR<0.001).

Based on these results, it can be concluded that methylation profiles ofNT-ESCs are much more similar to IVF-ESCs than to iPSCs. Both NT-ESCsand iPSCs do show evidence of residual HDF epigenetic memory, but iPSCscarry approximately 8-fold more of such sites. Interestingly, nearly 80%of DMPs in NT-ESCs, but only 12% in iPSCs, could be related to somaticepigenetic memory, suggesting that the majority of methylationabnormalities in iPSCs resulted from reprogramming errors.

Aberrant DNA Methylation at Imprinted Regions:

Imprinting is a form of epigenetic regulation that controls theexpression of distinct regions of the genome in aparent-of-origin-specific manner. Aberrant methylation of CpGdinucleotides at imprinted loci has been observed in iPSCs and in someIVF-ESCs (Nazor K L et al 2012 supra; Stelzer Y et al, Stem Cell Reports1, 79-89 (2013); and Rugg-Gunn P J et al, Human Mol Genet 16, R243-R251(2007)). Therefore, previously identified imprinted regions wereanalyzed (de Hoon M J et al, Bioinformatics 20, 1453-1454 (2004) andSaldanha, Bioinformatics 20, 3246-3248 (2004)). (FIG. 16A) For imprintedregions, CpG dinucleotides with a β value between 0.2 and 0.8 on the DNAmethylation microarray were considered to be partially methylated, asone would expect. Imprinted regions with β values above 0.8 wereconsidered to be aberrantly hypermethylated, and those below 0.2 werehypomethylated. It was first determined if the variance of the celllines was comparable to other independently generated cells within thepreviously identified imprinted regions based on CV calculations. TheCVs for the SCNT lines described herein ranged from 0.27-0.36 whereasthe lines described in Ziller et al 2011 supra ranged from 0.28-0.40.Unsupervised hierarchical clustering within imprinted regions showedthat NT-ESC lines clustered more closely with control IVF-ESCs anddisplayed a lower percentage of aberrantly methylated probes compared toiPSCs (Avg. percent of total imprinted probes aberrantly methylated iniPSCs=16.1%, NT-ESCs=10.4% and IVF-ESCs=7.9%; FIG. 16B). Several loci(DLGAP2, KCNK9, MKRN3) were hypermethylated in all three pluripotentstem cell types. However, differential expression of the associatedgenes was not observed at these loci.

NT-ESC-specific DNA methylation differences were also noted. All NT-ESCsdisplayed hypomethylation at the GNAS locus, while the NT2 and NT3 lineswere hypermethylated at the GNASAS/GNAS locus, and NT4 washypomethylated at the H19 locus (black boxes in FIG. 16A). Thehypomethylation of NT4 at H19 corresponded with biallelic expression ofthis gene.

All iPSC lines and hESO-7 displayed hypermethylated CpGs at the PEG3locus (yellow box in FIG. 16A) while only the iPSC lines displayedhypermethylated CpGs at the MEG3 locus (gray box in FIG. 2A) Thishypermethylation was associated with reduced expression of thecorresponding transcripts (black line on graphs in FIG. 16C; MEG3adjusted P-Val<0.001, Avg. Fold Change 19.8; PEG3 Adjusted P-Val<0.005,Avg. Fold Change 128.9; see colored bars on the histogram). The DIRAS3locus was also hypermethylated in all iPSCs, but was not correlated witha change in gene expression (white box in FIG. 16A).

DNA methylation abnormalities at imprinted loci associated with changesin gene expression were more frequent in iPSCs. In contrast, DNAmethylation profiles in NT-ESCs were more similar to IVF-ESC controls,suggesting more faithful reprogramming and better maintenance ofimprinting marks.

DNA Methylation at X-Chromosome Inactivated Sites:

X chromosome inactivation (XCI) results in monoallelic transcriptionalsilencing of genes on one of the X chromosomes in female cells, thusproviding X chromosome dosage compensation between males and females(reviewed in Lee J T and Bartolomei M S, Cell 152, 1308-1323 (2013)).Evidence of XCI can be detected by allele specific expression and Xchromosome coating by the long noncoding RNAs XIST and XACT) Silva S Set al, Proc Nat/Acad Sci USA 105, 4820-4825 (2008) and Vallot C et al,Nature Genet 45, 239-241 (2013)). The majority of human female IVF-ESCsdisplay evidence of XCI (Shen Y et al, Proc Nat/Acad Sci USA 105,4709-4714 (2008) and Tchieu J et al, Cell Stem Cell 7, 329-342 (2010)),with few exceptions Hanna J et al, Proc Nat/Acad Sci USA 107, 9222-9227(2010) and Marchetto M C et al, Cell 143, 527-539 (2010)). Based onRNA-Seq, it was determined that all ten female pluripotent stem celllines and HDFs expressed similar levels of XIST, but only thepluripotent cells expressed XACT.

DNA methylation differences between stem cell types at previouslyannotated XCI loci were assessed. As expected, the X chromosome heatmapprofile for the male line, hESO-8, was universally unmethylated (FIG.17A). β values for most of these loci for all female stem cell lines andthe somatic HDFs were between 0.2 and 0.8, consistent with partialmethylation, as expected in regions of XCI. NT-ESCs and IVF-ESCsdemonstrated, on average, higher levels of DNA methylation at XCI locicompared to parental HDFs, while methylation levels in iPSC lines weremarkedly and significantly higher than in NT-ESCs and female hESO-7(P-Value<0.001; FIG. 17B), with substantial variation among lines. Whenaberrant methylation was defined as β<0.2 or >0.8, all NT lines andhESO-7 had 4-fold fewer XCI methylation aberrations compared to iPSCs(P-Value<0.001; FIG. 3c ).

It was also examined whether aberrant DNA methylation at XCI sites wasassociated with alterations in gene expression. RNA-Seq demonstratedthat hypermethylation of POU3F4, SLITRK2 and SLITRK4 in the iPS-R2 linecorresponded to lower levels of gene expression (black boxes in FIG.17A), indicating that the relative genetic stability (no CNVs) of thiscell line did not correlate with epigenetic integrity. In addition,hypomethylation of DACH2, RPS6KA6 and CHM in iPS-R1 and TMEM187 iniPS-S2 correlated with increased gene expression (white boxes in FIG.17A). Aberrant DNA methylation associated with alterations in geneexpression of tumor associated genes, such as the SLITRK gene family(Aruga J et al, Gene 315, 87-94 (2003)), emphasizes the need forthorough quality-control measures on stem cells destined for clinicaluse.

DNA Methylation at Autosomal Non-Imprinted Loci:

DNA methylation analysis of autosomal non-imprinted CpG and non-CpGsites using the Kruskal-Wallis test revealed 1,621 DMPs among NT-ESCs,iPSCs and IVF-ESCs (P-Value<0.01, Δβ>0.5). We grouped these probes intosix major clusters using an unsupervised self-organizing map algorithm(Newman A M and Cooper J B, BMC Bioinformatics 11, 117 (2010)). All sixclusters were analyzed for cis-regulatory functional enrichments usingGREAT (McLean C Y et al, Nature Biotechnol 28, 495-501 (2010)), but onlyCluster 3 showed significant enrichments for categories associated withmorphogenesis and neural development iPSCs displayed higher DNAmethylation levels compared to NT-ESCs and IVF-ESCs for most clusters,with the exception of Cluster 4. NT-ESCs displayed an intermediate DNAmethylation pattern between iPSCs and IVF-ESCs, but were overall closerto IVF-ESCs.

Several different probe subsets were examined. Higher methylation levelsamong iPSC lines compared to IVF-ESC lines were observed, consistentwith previous reports (Nishino K et al, PLoS Genetics, 7, e1002085(2011); and Polo J M et al, Nat Biotech 28, 848-855 (2010); both ofwhich are incorporated by reference herein.) The examined subsetsincluded: probes located within −2000 bp of the transcription start site(TSS); CpG islands (CGI); 5′ and 3′ regions (0-2 kb from CGI and 2-4 kbfrom CGI)(Doi A et al, Nature Genet 41, 1350-1353 (2009) and Irizarry RA et al, Nat Genet 41, 178-186 (2009)); FANTOM 4 promoters with low andhigh CpG content (http://fantom.gsc.riken.jp/4/); predicted enhancers(Consortium E P et al, Nature 447, 799-816 (2007); Heintzman N. D. etal, Nature Genet 39, 311-318 (2007); and Heintzman N D et al, Nature459, 108-112 (2009)); major histocompatibility complex regions (TomazouE M et al, BMC Med Genom 1, 19 (2008)); C-DMRs (cancer-related DMRs) andR-DMRs (reprogramming-related DMRs); and repetitive elements. Thelargest difference between iPSCs and NT/IVF-ESCs was apparent in R-DMRs,where iPSCs were very similar to parental HDFs. This finding issurprising, as R-DMRs were previously reported to be differentiallymethylated between iPSCs and fibroblasts.

Aberrant Reprogramming of CG Methylation Detected by Whole GenomeBisulfite Sequencing:

To gain a more detailed picture of the underlying methylationdifferences between the NT-ESC and iPSC lines, high-coveragebase-resolution methylomes of the matched HDF-derived stem cell linesand IVF-ESC controls (coverage ranged from 14× to 25×) were generatedusing MethylC-Seq. The data were then compared to existing wholemethylome data from three additional IVF-ESC lines (H1, H9 and HUES6)described in earlier publications Xie W et al, Cell 153, 1134-1148(2013); Laurent L et al, Genome Res 20, 320-331 (2010); and Lister R etal, Science 341, 1237905 (2013)). Hierarchical clustering of themethylation level at CG-DMRs demonstrated that the CG methylationlandscape of NT-ESCs more closely resembled that of the IVF-ESCscompared to the iPSCs (FIG. 18A). By comparing the methylomes of allIVF-ESCs, NT-ESCs, iPSCs and filtering regions that were obscure inmethylation pattern or highly variable in IVF-ESCs, a total of 678CG-DMRs were identified that were present in at least one NT-ESC or iPSCline but not in IVF-ESCs (FDR=0.01, also see methods). The majority ofthese CG-DMRs were identified within iPSCs (619), while NT-ESCscontained 3-fold fewer (212). A total of 153 CG-DMRs were shared betweenboth cell types (FIG. 18B). Using similar CG-DMR screening approach itwas calculated that five iPSC lines previously profiled carried a totalof 792 CG-DMR suggesting that both iPSC groups are comparable. Detailedanalysis revealed that most of these CG-DMRs were localized within CGislands and gene bodies (FIG. 18C). Analysis of CG-DMR distributionamong individual cell lines showed that each NT-ESC line had feweraberrant CG methylation regions than any of the iPSC lines, againimplying that the NT-ESCs were more similar to controls (FIG. 18D,p-value=0.0147, Mann-Whitney test). CG-DMRs were then assigned intothree groups: memory DMRs (mDMRs) that were shared with HDFs;NT-specific (ntDMRs) and iPSC-specific DMRs (iDMRs). Comparing thenumber of mDMRs and cell specific DMRs, it was found that on average,38% of total CG-DMRs in the NT-ESC lines were of somatic memory originwhile 22% of DMRs in iPSCs were of somatic memory origin (FIG. 4D).

Inspection of the recurrent CG-DMRs (hotspot DMRs) that were identifiedin every iPSC or NT-ESC line revealed that the four NT-ESC lines had 50hotspot DMRs, which was 2-fold less than the 104 hotspot DMRs present inall four iPSC lines (FIG. 18E). Interestingly, 48 of 50 hotspot DMRsidentified among NT-ESCs were also shared with iPSCs (p-value<0.001,Hypergeometric test). Further analysis of these hotspot DMRs sharedamong all 8 cell lines revealed that 63% (30 out of 48) were mDMRs. Thissuggests that most hotspot DMRs common to both NT-ESCs and iPSCsrepresent regions resistant to reprogramming by either approach. Only 2out of 50 (4%) hotspot DMRs were unique to NT-ESCs compared to 56 out of104 (54%) iPSCs specific hotspots (FIG. 18E). This implies that SCNT isassociated with fewer de novo aberrant CG methylation events compared tothe iPSC reprogramming method.

NT-ESCs display less aberrant non-CG methylation than iPSCs:

Pervasive and exclusive non-CG methylation has been identified inpluripotent stem cells compared to fibroblasts. In addition, iPSCs carryfrequent aberrant non-CG methylation in megabase-scale regions. Hereinit is demonstrated that the only regions on the methylation array atwhich iPSCs were consistently hypomethylated compared to NT/IVF-ESCswere the non-CpG sites, including “mega-DMRs” (FIG. 19A and FIG. 19B).At the 110 non-CpG sites in mega-DMRs interrogated by the InfiniumHumanMethylation450 BeadChip®, iPSCs were significantly hypomethylatedcompared to IVF-ESCs (P<0.001, Mann-Whitney test), whereas there was nosignificant difference between NT-ESCs and IVF-ESCs. Since non-CpGmethylation is markedly more prevalent in pluripotent cells compared tofibroblasts, these results are consistent with the notion that SCNTresults in more complete reprogramming than does standard transcriptionfactor-based reprogramming.

To investigate the extent of non-CG methylation in more detail, regionsshowing large-scale non-CG methylation differences in the reprogrammedcell lines when compared to IVF-ESC were systematically identified. FiveIVF-ESC lines served as the gold standard methylation landscape forpluripotent stem cells. A total of 150 autosomal non-CG mega-DMRs wereidentified when the methylomes of the four NT-ESCs nine iPSCs werecompared to controls. Non-CG mega-DMRs linked to the sex chromosomeswere excluded from this study due to the mixed gender of the fiveIVF-ESC controls. These non-CG mega-DMRs covered 123 Mb of genome andincluded all of the regions reported in the previous study (99% ofbases). Of the total 150 non-CG mega-DMRs identified in the combineddataset, 77 were identified in both NT-ESCs and iPSCs from this study,of which 75 occurred exclusively in iPSCs (FIG. 19A). These DMRs weredistributed on every autosomal chromosome except chromosome 13 (FIG.19B). Only 7 non-CG mega-DMRs (10-fold less) were present in NT-ESCs andwere localized on four chromosomes (FIG. 19A and FIG. 19B). Non-CGmega-DMRs were shown to be significantly closer to centromeric andtelomeric regions compared with shuffled non-CG mega-DMRs (FIG. 19B,p-value<0.001). Several different patterns of aberrant non-CGmethylation were observed including hypomethylation in iPSCs only,hypomethylation in both NT-ESCs and iPSCs, and hypermethylation in iPSCsonly. However, the vast majority of non-CG mega-DMRs (79.6%, or 92.5% oftotal bases) were hypomethylated in iPSCs and/or NT-ESCs compared withIVF-ESCs (FIG. 19C).

iPSCs described herein were determined to similar to other iPSCs whencompared to iPSC lines generated previously. The four iPSC lines fromthis study contained a total of 75 DMRs, while the five iPSC linesgenerated earlier carried 121 non-CG mega-DMRs. This indicates thatdespite different somatic cell origins and possible culture differencesin different laboratories, iPSC lines carry similar levels of aberrantnon-CG methylation. In contrast, the NT-ESCs showed less aberrant non-CGmethylation compared to all iPSCs (FIG. 19C and FIG. 19D, p-value<0.005,Mann-Whitney test). Hierarchical clustering of the iPSC and NT-ESCs bynon-CG methylation state for all non-CG mega-DMRs also supported theconclusion that the NT-ESCs are more similar to IVF-ESCs than the iPSCs.

To understand the functional impact of non-CG mega-DMRs, transcriptionalactivity within those regions was examined. On average, 2 genes inNT-ESCs and 30 in iPSCs were located within non-CG mega DMRs, implyingthat fewer genes in NT-ESCs are under potential disruption bymethylation (p-value=0.0147, Mann-Whitney test). GO analysis (Gore A etal, Nature 471, 63-67 (2011)) for genes in hypomethylated non-CG DMRsrevealed that these genes were enriched in categories related toolfactory transduction, epidermal cell differentiation, cytoskeleton,Immunoglobulin and Homeobox protein (FDR≦0.001). Gene expression in theiPSCs for 2 genes in the hypermethylated non-CG mega-DMRs wasupregulated whereas expression of 24 genes in the iPSCs and 6 genes inthe NT-ESCs in the hypomethylated non-CG mega-DMRs was down regulated,consistent with previous findings (p-value<0.001). Taken together, theseobservations indicate that in non-CG methylation regions, NT-ESCs weremore faithfully reprogrammed to a state that more closely resembled thatof the gold standard IVF-ESCs compared to the iPSCs. Among the NT-ESCs,NT4 had the least aberrant methylations in both CG and non-CG contexts.

Global Gene Expression:

Lastly global gene expression patterns from strand-specific RNA-Seq werecompared. Consistent with DNA methylation, intra-group variability wassimilar among the three pluripotent cell types (CVs: NT-ESC=1.41,IVF-ESC=1.45, IPSC=1.44) and unsupervised hierarchical clustering withbootstrap resampling indicated that, in contrast to iPSCs, NT-ESCsclustered closely with IVF-ESCs (FIG. 20A). Differential expressionanalysis (FDR<0.05) among the pluripotent stem cell types yielded1220925 transcripts, which were grouped into 10 clusters by unsupervisedclustering. The majority (65%) of these genes were either significantlyup- or down-regulated in iPSCs compared to NT-ESCs and IVF-ESCs.Clusters 2 and 3 showed higher gene expression in NT-ESCs and IVF-ESCscompared to iPSCs. When subjected to functional enrichment analysis,these clusters were associated with p38 MAPK signaling pathway((FDR=0.02; n=51) and Krueppel-associated box genes (FDR=0.001; n=91),respectively. Cluster 10 contained transcripts that were up-regulated inIVF-ESCs compared to both NT-ESCs and iPSCs. This cluster included genesassociated with Zinc Finger and C2H2-like genes (FDR=0.002; n=227).Transcripts in Cluster 8 were enriched for MGI expression of TS10primary trophoblast giant cells (FDR=0.03; n=46). Genes in cluster 5,associated with Y-linked inheritance, were up-regulated in one pair ofmale IVF-ESCs.

Based on the differential expression analysis results (FIG. 20A),evidence of transcriptional memory was observed. To find which genesdisplayed transcriptional memory in both our iPSC lines and NT-ESClines, three separate t-tests were conducted between the HDF samples andthe IVF-ESC lines, the NT-ESC lines and the IVF-ESC lines and the iPSClines and the IVF-ESC lines at a FDR cutoff of 0.05. Genes that weredifferentially expressed in both the HDFs and NT-ESCs or iPSC lines werealso identified. A total of 24 genes were expressed at significantlylower levels in the NT-ESCs and HDFs compared to IVF-ESCs. Theserepresented genes that were potentially incompletely reactivated duringreprogramming. A total of 12 genes were expressed at significantlyhigher levels in the NT-ESCs and HDFs compared to IVF-ESCs. Theserepresented genes that were potentially incompletely silenced duringreprogramming (FIG. 20B). In comparison, 171 genes in the iPSC linesthat were potentially incompletely reactivated and 32 genes that werepotentially incompletely silenced (FIG. 20B). Therefore, the number ofaffected genes was markedly higher in the iPSCs compared to the NT-ESCs.

It was then examined whether the genes that exhibited transcriptionalmemory also showed promoter DNA methylation differences. Only the genesthat were incompletely reactivated in our iPSC lines possessedsignificantly different methylation in their promoter regions(Mann-Whitney test p<2.2×10⁻¹⁶) when compared to IVF-ESC lines (FIG.20C). This suggests that incomplete demethylation of promoter regionscan have occurred during iPSC generation and resulted in transcriptionaldifferences between our iPSCs and IVF-ESCs. Overall, the gene expressionand DNA methylation results were consistent, and both suggested thatNT-ESC lines are markedly more similar to IVF-ESCs than to iPSCs.

1. A method of producing a human pluripotent embryonic stem cell, themethod comprising: enucleating a human oocyte obtained from an oocytedonor by removing the MII spindle in a manner that does not lower levelsof maturation promoting factor, thereby producing a cytoplast;contacting a human donor nucleus with an HVJ-E extract; contacting thecytoplast with the human donor nucleus thereby producing an SCNT embryo;treating the human oocyte and/or the cytoplast and/or the donor nucleusand/or the SCNT embryo with at least 0.5 mM caffeine; applying a firstelectroporation pulse to the SCNT embryo, thereby producing an activatedSCNT embryo; culturing the activated SCNT embryo in a first mediacomprising 6-DMAP; culturing the activated SCNT embryo in a second mediacomprising TSA; culturing the activated SCNT embryo in a third mediathereby producing a blastocyst; culturing the blastocyst on a feederlayer; selecting a cell with an embryonic stem cell-like morphology. 2.The method of claim 1 wherein the human oocyte was obtained from adonation cycle of 15 or fewer oocytes.
 3. The method of claim 1 whereinthe human oocyte was obtained from an oocyte donor previously treatedwith a GnRH antagonist.
 4. The method of claim 3 wherein the GnRHantagonist comprises ganirelix.
 5. The method of claim 1 furthercomprising obtaining the human oocyte from the oocyte donor.
 6. Themethod of claim 1 wherein removing the MII spindle is performed using apolarized microscope.
 7. The method of claim 1 wherein the donor nucleusis included within a donor cell.
 8. The method of claim 7 furthercomprising contacting the donor cell with trypsin thereby producing adisaggregated donor cell.
 9. The method of claim 1 wherein treating withthe protein phosphatase inhibitor occurs during both enucleation of thehuman oocyte and contacting the SCNT embryo with the donor nucleus. 10.The method of claim 1 wherein the protein phosphatase inhibitorcomprises caffeine.
 11. The method of claim 1 further comprisingtreating the human oocyte and/or the enucleated oocyte and/or the SCNTembryo with between 0.5 mM and 2.5 mM caffeine.
 12. The method of claim1 further comprising applying a second electroporation pulse.
 13. Themethod of claim 12 wherein the first electroporation pulse is a 50 μs DCpulse of 2.7 kV cm⁻¹ and wherein the second electroporation pulse is a50 μs DC pulse of 2.7 kV cm⁻¹.
 14. The method of claim 1 wherein thefirst media comprises at least 2 mM 6-DMAP.
 15. The method of claim 14further comprising culturing the activated SCNT embryo in the firstmedia for at least 4 hours.
 16. The method of claim 1 wherein the secondmedia comprises at least 10 mM TSA.
 17. The method of claim 1 whereinthe third media comprises BSA and β-mercaptoethanol.
 18. The method ofclaim 1 further comprising characterizing the selected cells withembryonic stem-cell like morphologies as human pluripotent embryonicstem cells comprising donor nucleus nuclear DNA and oocyte donormitochondrial DNA.